Mercurial > repos > ppericard > mixomics_blocksplsda

annotate Integration_block_splsda_fonc.R @ 3:0a3c83f2197a draft

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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
author ppericard
date Fri, 25 Oct 2019 07:10:59 -0400
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1 # La fonction meanSpotRepl remplace les valeurs des spots répliqués par la
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2 # moyenne de leurs intensités.
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4 meanSpotRepl <-function(mat)
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5 {
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6 ProbeName = colnames(mat)
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7 isDup = duplicated(ProbeName)
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8 dupNames = ProbeName[isDup]
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10 for (dups in unique(dupNames))
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11 {
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12 mat[dups,] = apply(mat[which(colnames(mat) == dups), ], 2, mean)
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14 }
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16 res = mat[, -which(isDup)] # On retire de la matrice mat toutes les spots qui sont répliqués.
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18 return(res)
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20 }
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22 # La fonction supprimerVaConst supprime de la matrice mat les variables constantes.
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24 supprimerVaConst <-function(mat)
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25 {
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26 name_mat = deparse(substitute(mat))
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28 cat(paste0("Pour ", name_mat, ", avant suppression des variables constantes, il y a ", dim(mat)[2], " variables."), "\n")
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30 indiceVaConst = sapply(1:dim(mat)[2], FUN = function(i){
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31 col_mat_i = mat[, i]
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32 res = all(col_mat_i == col_mat_i[1])
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34 return(res)
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35 })
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37 if(length(which(indiceVaConst == FALSE)) != 0)
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38 {
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39 res = mat[, which(indiceVaConst == FALSE)]
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41 }else{
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42 res = mat
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44 }
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46 cat(paste0("Pour ", name_mat, ", après suppression des variables constantes, il reste ", dim(res)[2], " variables."), "\n")
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48 return(res)
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49 }
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51 # La fonction supprimerVaNaInd supprime les variables contenant des NA
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52 # (si on garde les NA dans ces variables, les composantes du bloc ne
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53 # sont plus orthogonales).
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55 supprimerVaNaInd <-function(mat)
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56 {
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57 indiceVaNaInd = sapply(1:dim(mat)[2], FUN = function(i){
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58 col_mat_i = mat[, i]
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60 indNA = length(which(is.na(col_mat_i) == TRUE))
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62 if(indNA >= 1)
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63 {
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64 res = FALSE
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66 }else{
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67 res = TRUE
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69 }
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71 return(res)
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72 })
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74 mat2 = mat[, which(indiceVaNaInd == TRUE)]
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75 name_mat = deparse(substitute(mat))
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77 cat(paste0("Pour ", name_mat, ", après suppression des variables contenant des NA, il reste ", dim(mat2)[2], " variables."), "\n")
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79 return(mat2)
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81 }
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83
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84 # La fonction varAnnotation permet de fournir des informations sur les variables
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85 # sélectionnées pour un design.
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86
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87 varAnnotation <-function(variablesSelect,
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88 data_transcripto_col,
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89 annot_metageno_caecum)
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90 {
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91 res_variablesSelect = variablesSelect
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93 noms_blocks = sapply(1:length(variablesSelect), FUN = function(i){
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94 ch = strsplit(names(variablesSelect)[i], split = "_")[[1]]
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95
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96 if(ch[1] == "resBio")
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97 {
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98 res = "resBio"
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99
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100 }else{
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101 res = paste(ch[1:2], collapse = "_")
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102
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103 }
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104
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105 return(res)
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106 })
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107
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108 ind_transcripto_col = which(noms_blocks == "transcripto_col")
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109
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110 if(length(variablesSelect[[ind_transcripto_col]]) != 0)
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111 {
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112
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113
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114 varSelect_transcripto_colTemp = variablesSelect[[ind_transcripto_col]]
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115 varSelect_transcripto_col = sapply(1:length(varSelect_transcripto_colTemp), FUN = function(i){
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116 ch = strsplit(varSelect_transcripto_colTemp[i], split = "_")[[1]]
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117
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118 res = paste(ch[2:length(ch)], collapse = "_")
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119
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120 return(res)
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121 })
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122
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123 dataframe_varSelect_transcripto_col = data.frame(ProbeName = varSelect_transcripto_col)
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124
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125 dataframe_annot_transcripto_col = data.frame(ProbeName = data_transcripto_col$genes$ProbeName,
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126 GeneName = data_transcripto_col$genes$GeneName,
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127 Description = data_transcripto_col$genes$Description,
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128 SystematicName = data_transcripto_col$genes$SystematicName)
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129
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130 tab_transcripto_col = join(x = dataframe_varSelect_transcripto_col, y = dataframe_annot_transcripto_col,
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131 type = "inner",
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132 by = "ProbeName")
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133
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134 res_variablesSelect[[ind_transcripto_col]] = tab_transcripto_col
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135
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136
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137 }
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138
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139 ind_metageno_caecum = which(noms_blocks == "metageno_caecum")
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140
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141 if(length(variablesSelect[[ind_metageno_caecum]]) != 0)
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142 {
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143 varSelect_metageno_caecum_Temp1 = variablesSelect[[ind_metageno_caecum]]
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144 varSelect_metageno_caecum_Temp2 = sapply(1:length(varSelect_metageno_caecum_Temp1), FUN = function(i){
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145 ch = strsplit(varSelect_metageno_caecum_Temp1[i], split = "")[[1]]
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146
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147 if(ch[1] == "X")
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148 {
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149 res = paste(ch[2:length(ch)], collapse = "")
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150
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151 }else{
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152 res = varSelect_metageno_caecum_Temp1[i]
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153
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154 }
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155
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156 return(res)
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157 })
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158
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159
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160 dataframe_varSelect_metageno_caecum = data.frame(taxon = varSelect_metageno_caecum_Temp2)
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161
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162 dataframe_annot_metageno_caecum = data.frame(annot_metageno_caecum)
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163 colnames(dataframe_annot_metageno_caecum)[1] = "taxon"
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164
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165 tab_metageno_caecum = join(x = dataframe_varSelect_metageno_caecum, y = dataframe_annot_metageno_caecum,
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166 type = "inner",
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167 by = "taxon")
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168
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169 res_variablesSelect[[ind_metageno_caecum]] = tab_metageno_caecum
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170
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171
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172 }
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173
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174 ind_metabo_S1 = which(noms_blocks == "metabo_S1")
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175
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176 if(length(variablesSelect[[ind_metabo_S1]]) != 0)
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177 {
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178 res_variablesSelect[[ind_metabo_S1]] = data.frame(variable = variablesSelect[[ind_metabo_S1]])
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179
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180 }
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181
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182 ind_resBio = which(noms_blocks == "resBio")
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183
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184 if(length(variablesSelect[[ind_resBio]]) != 0)
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185 {
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186 res_variablesSelect[[ind_resBio]] = data.frame(variable = variablesSelect[[ind_resBio]])
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187
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188 }
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189
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190
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191 return(res_variablesSelect)
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192
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193
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194 }
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195
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196
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197 # La fonction varAnnotation_gene_6blocks permet de fournir des informations sur les variables
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198 # sélectionnées pour un design.
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199
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200 varAnnotation_gene_6blocks <-function(variablesSelect,
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201 data_transcripto_col,
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202 data_transcripto_tae,
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203 annot_metageno_caecum,
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204 metavar_metaboLC_S1,
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205 metavar_resBio,
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206 metavar_cyto)
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207 {
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208 res_variablesSelect = variablesSelect
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209 noms_blocks = names(variablesSelect)
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210
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211 ind_transcripto_col = which(noms_blocks == "transcripto_col")
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212
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213 if(length(ind_transcripto_col) != 0)
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214 {
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215
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216 varSelect_transcripto_colTemp = variablesSelect[[ind_transcripto_col]]
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217
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218 if(length(varSelect_transcripto_colTemp) != 0)
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219 {
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220 varSelect_transcripto_col = sapply(1:length(varSelect_transcripto_colTemp), FUN = function(i){
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221 variable_i = varSelect_transcripto_colTemp[i]
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222 res = gsub("Colon_", "", variable_i, fixed = TRUE)
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223
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224 return(res)
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225 })
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226
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227 dataframe_varSelect_transcripto_col = data.frame(GeneName = varSelect_transcripto_col)
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228
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229 dataframe_annot_transcripto_col = data.frame(ProbeName = data_transcripto_col$genes$ProbeName,
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230 GeneName = data_transcripto_col$genes$GeneName,
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231 Description = data_transcripto_col$genes$Description,
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232 SystematicName = data_transcripto_col$genes$SystematicName)
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233
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234 tab_transcripto_col = join(x = dataframe_varSelect_transcripto_col, y = dataframe_annot_transcripto_col,
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235 type = "inner",
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236 by = "GeneName")
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237
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238 res_variablesSelect[[ind_transcripto_col]] = tab_transcripto_col
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239
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240 }else{
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241 res_variablesSelect[[ind_transcripto_col]] = ""
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242
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243 }
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244
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245
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246
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247
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248 }
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249
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250 ind_transcripto_tae = which(noms_blocks == "transcripto_tae")
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251
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252 if(length(ind_transcripto_tae) != 0)
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253 {
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254
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255 varSelect_transcripto_taeTemp = variablesSelect[[ind_transcripto_tae]]
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256
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257 if(length(varSelect_transcripto_taeTemp) != 0)
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258 {
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259 varSelect_transcripto_tae = sapply(1:length(varSelect_transcripto_taeTemp), FUN = function(i){
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260 variable_i = varSelect_transcripto_taeTemp[i]
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261 res = gsub("TAE_", "", variable_i, fixed = TRUE)
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262
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263 return(res)
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264 })
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265
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266 dataframe_varSelect_transcripto_tae = data.frame(GeneName = varSelect_transcripto_tae)
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267
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268 dataframe_annot_transcripto_tae = data.frame(ProbeName = data_transcripto_tae$genes$ProbeName,
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269 GeneName = data_transcripto_tae$genes$GeneName,
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270 Description = data_transcripto_tae$genes$Description,
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271 SystematicName = data_transcripto_tae$genes$SystematicName)
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272
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273 tab_transcripto_tae = join(x = dataframe_varSelect_transcripto_tae, y = dataframe_annot_transcripto_tae,
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274 type = "inner",
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275 by = "GeneName")
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276
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277 res_variablesSelect[[ind_transcripto_tae]] = tab_transcripto_tae
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278
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279 }else{
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280 res_variablesSelect[[ind_transcripto_tae]] = ""
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281
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282
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283 }
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285
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286
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287
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288 }
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289
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290
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291 ind_metageno_caecum = which(noms_blocks == "metageno_caecum")
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292
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293 if(length(ind_metageno_caecum) != 0)
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294 {
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295 varSelect_metageno_caecum_Temp1 = variablesSelect[[ind_metageno_caecum]]
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296
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297 if(length(varSelect_metageno_caecum_Temp1) != 0)
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298 {
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299 varSelect_metageno_caecum_Temp2 = sapply(1:length(varSelect_metageno_caecum_Temp1), FUN = function(i){
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300 ch = strsplit(varSelect_metageno_caecum_Temp1[i], split = "")[[1]]
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301
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302 if(ch[1] == "X")
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303 {
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304 res = paste(ch[2:length(ch)], collapse = "")
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305
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306 }else{
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307 res = varSelect_metageno_caecum_Temp1[i]
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308
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309 }
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310
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311 return(res)
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312 })
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313
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314
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315 dataframe_varSelect_metageno_caecum = data.frame(taxon = varSelect_metageno_caecum_Temp2)
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316
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317 dataframe_annot_metageno_caecum = data.frame(annot_metageno_caecum)
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318 colnames(dataframe_annot_metageno_caecum)[1] = "taxon"
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319
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320 tab_metageno_caecum = join(x = dataframe_varSelect_metageno_caecum, y = dataframe_annot_metageno_caecum,
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321 type = "inner",
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322 by = "taxon")
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323
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324 res_variablesSelect[[ind_metageno_caecum]] = tab_metageno_caecum
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325
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326 }else{
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327 res_variablesSelect[[ind_metageno_caecum]] = ""
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328
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329
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330 }
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331
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332
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333
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334
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335 }
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336
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337 ind_metaboLC_S1 = which(noms_blocks == "metaboLC_S1")
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338
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339 if(length(ind_metaboLC_S1) != 0)
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340 {
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341 if(length(variablesSelect[[ind_metaboLC_S1]]) != 0)
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342 {
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343 res_variablesSelect[[ind_metaboLC_S1]] = data.frame(variable = variablesSelect[[ind_metaboLC_S1]])
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344
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345 }else{
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346 res_variablesSelect[[ind_metaboLC_S1]] = ""
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347
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348 }
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349
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350
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351 }
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352
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353 ind_resBio = which(noms_blocks == "resBio")
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354
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355 if(length(ind_resBio) != 0)
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356 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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357 if(length(variablesSelect[[ind_resBio]]) != 0)
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358 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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359 res_variablesSelect[[ind_resBio]] = data.frame(variable = variablesSelect[[ind_resBio]])
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360
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361 }else{
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362 res_variablesSelect[[ind_resBio]] = ""
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363
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364 }
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365
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366
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367 }
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368
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369 ind_cyto = which(noms_blocks == "cyto")
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370
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371 if(length(ind_cyto) != 0)
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372 {
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373 if(length(variablesSelect[[ind_cyto]]) != 0)
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374 {
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375 res_variablesSelect[[ind_cyto]] = data.frame(variable = variablesSelect[[ind_cyto]])
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376
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377 }else{
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378 res_variablesSelect[[ind_cyto]] = ""
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379
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380 }
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381
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382
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383 }
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384
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385
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diff changeset
386 return(res_variablesSelect)
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387
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388
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389 }
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390
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391 # La fonction varAnnotation_gene_6blocks permet de fournir des informations sur les variables
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392 # sélectionnées pour un design.
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393
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394 varAnnotation_gene_6blocks <-function(variablesSelect,
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diff changeset
395 data_transcripto_col,
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396 data_transcripto_tae,
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397 annot_metageno_caecum,
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398 metavar_metaboLC_S1,
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diff changeset
399 metavar_resBio,
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400 metavar_cyto)
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401 {
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402 res_variablesSelect = variablesSelect
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403 noms_blocks = names(variablesSelect)
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404
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405 ind_transcripto_col = which(noms_blocks == "transcripto_col")
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406
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407 if(length(ind_transcripto_col) != 0)
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408 {
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409
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410 varSelect_transcripto_colTemp = variablesSelect[[ind_transcripto_col]]
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411
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412 if(length(varSelect_transcripto_colTemp) != 0)
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413 {
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414 varSelect_transcripto_col = sapply(1:length(varSelect_transcripto_colTemp), FUN = function(i){
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415 variable_i = varSelect_transcripto_colTemp[i]
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416 res = gsub("Colon_", "", variable_i, fixed = TRUE)
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417
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418 return(res)
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419 })
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420
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421 dataframe_varSelect_transcripto_col = data.frame(GeneName = varSelect_transcripto_col)
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422
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423 dataframe_annot_transcripto_col = data.frame(ProbeName = data_transcripto_col$genes$ProbeName,
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424 GeneName = data_transcripto_col$genes$GeneName,
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425 Description = data_transcripto_col$genes$Description,
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426 SystematicName = data_transcripto_col$genes$SystematicName)
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427
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428 tab_transcripto_col = join(x = dataframe_varSelect_transcripto_col, y = dataframe_annot_transcripto_col,
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429 type = "inner",
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430 by = "GeneName")
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431
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432 res_variablesSelect[[ind_transcripto_col]] = tab_transcripto_col
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433
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434 }else{
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435 res_variablesSelect[[ind_transcripto_col]] = ""
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436
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437 }
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438
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439
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440
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441
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442 }
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443
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444 ind_transcripto_tae = which(noms_blocks == "transcripto_tae")
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445
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446 if(length(ind_transcripto_tae) != 0)
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447 {
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448
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449 varSelect_transcripto_taeTemp = variablesSelect[[ind_transcripto_tae]]
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450
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451 if(length(varSelect_transcripto_taeTemp) != 0)
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452 {
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453 varSelect_transcripto_tae = sapply(1:length(varSelect_transcripto_taeTemp), FUN = function(i){
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454 variable_i = varSelect_transcripto_taeTemp[i]
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455 res = gsub("TAE_", "", variable_i, fixed = TRUE)
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456
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457 return(res)
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458 })
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459
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460 dataframe_varSelect_transcripto_tae = data.frame(GeneName = varSelect_transcripto_tae)
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461
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462 dataframe_annot_transcripto_tae = data.frame(ProbeName = data_transcripto_tae$genes$ProbeName,
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463 GeneName = data_transcripto_tae$genes$GeneName,
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464 Description = data_transcripto_tae$genes$Description,
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465 SystematicName = data_transcripto_tae$genes$SystematicName)
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466
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467 tab_transcripto_tae = join(x = dataframe_varSelect_transcripto_tae, y = dataframe_annot_transcripto_tae,
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468 type = "inner",
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diff changeset
469 by = "GeneName")
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470
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471 res_variablesSelect[[ind_transcripto_tae]] = tab_transcripto_tae
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472
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473 }else{
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474 res_variablesSelect[[ind_transcripto_tae]] = ""
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475
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476
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477 }
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478
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parents:
diff changeset
479
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
480
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
481
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
482 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
483
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
484
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
485 ind_metageno_caecum = which(noms_blocks == "metageno_caecum")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
486
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
487 if(length(ind_metageno_caecum) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
488 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
489 varSelect_metageno_caecum_Temp1 = variablesSelect[[ind_metageno_caecum]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
490
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
491 if(length(varSelect_metageno_caecum_Temp1) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
492 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
493 varSelect_metageno_caecum_Temp2 = sapply(1:length(varSelect_metageno_caecum_Temp1), FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
494 ch = strsplit(varSelect_metageno_caecum_Temp1[i], split = "")[[1]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
495
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
496 if(ch[1] == "X")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
497 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
498 res = paste(ch[2:length(ch)], collapse = "")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
499
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
500 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
501 res = varSelect_metageno_caecum_Temp1[i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
502
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
503 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
504
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
505 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
506 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
507
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
508
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
509 dataframe_varSelect_metageno_caecum = data.frame(taxon = varSelect_metageno_caecum_Temp2)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
510
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
511 dataframe_annot_metageno_caecum = data.frame(annot_metageno_caecum)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
512 colnames(dataframe_annot_metageno_caecum)[1] = "taxon"
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
513
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
514 tab_metageno_caecum = join(x = dataframe_varSelect_metageno_caecum, y = dataframe_annot_metageno_caecum,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
515 type = "inner",
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
516 by = "taxon")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
517
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
518 res_variablesSelect[[ind_metageno_caecum]] = tab_metageno_caecum
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
519
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
520 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
521 res_variablesSelect[[ind_metageno_caecum]] = ""
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
522
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
523
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
524 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
525
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
526
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
527
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
528
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
529 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
530
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
531 ind_metaboLC_S1 = which(noms_blocks == "metaboLC_S1")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
532
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
533 if(length(ind_metaboLC_S1) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
534 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
535 if(length(variablesSelect[[ind_metaboLC_S1]]) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
536 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
537
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
538 dataframe_varSelect_metaboLC_S1 = data.frame(Variable = variablesSelect[[ind_metaboLC_S1]])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
539 dataframe_metavar_metaboLC_S1 = data.frame(metavar_metaboLC_S1)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
540
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
541
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
542 dataframe_metavar_varSelect_metaboLC_S1 = join(x = dataframe_varSelect_metaboLC_S1, y = dataframe_metavar_metaboLC_S1,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
543 type = "inner",
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
544 by = "Variable")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
545
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
546 res_variablesSelect[[ind_metaboLC_S1]] = dataframe_metavar_varSelect_metaboLC_S1
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
547
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
548 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
549 res_variablesSelect[[ind_metaboLC_S1]] = ""
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
550
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
551 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
552
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
553 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
554
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
555
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
556 ind_resBio = which(noms_blocks == "resBio")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
557
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
558 if(length(ind_resBio) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
559 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
560 if(length(variablesSelect[[ind_resBio]]) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
561 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
562
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
563 dataframe_varSelect_resBio = data.frame(Variable = variablesSelect[[ind_resBio]])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
564 dataframe_metavar_resBio = data.frame(metavar_resBio)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
565
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
566
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
567 dataframe_metavar_varSelect_resBio = join(x = dataframe_varSelect_resBio, y = dataframe_metavar_resBio,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
568 type = "inner",
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
569 by = "Variable")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
570
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
571 res_variablesSelect[[ind_resBio]] = dataframe_metavar_varSelect_resBio
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
572
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
573 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
574 res_variablesSelect[[ind_resBio]] = ""
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ppericard
parents:
diff changeset
575
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
576 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
577
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
578 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
579
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
580 ind_cyto = which(noms_blocks == "cyto")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
581
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
582 if(length(ind_cyto) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
583 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
584 if(length(variablesSelect[[ind_cyto]]) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
585 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
586
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
587 dataframe_varSelect_cyto = data.frame(Variable = variablesSelect[[ind_cyto]])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
588 dataframe_metavar_cyto = data.frame(metavar_cyto)
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ppericard
parents:
diff changeset
589
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
590
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
591 dataframe_metavar_varSelect_cyto = join(x = dataframe_varSelect_cyto, y = dataframe_metavar_cyto,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
592 type = "inner",
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
593 by = "Variable")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
594
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
595 res_variablesSelect[[ind_cyto]] = dataframe_metavar_varSelect_cyto
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
596
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
597 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
598 res_variablesSelect[[ind_cyto]] = ""
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
599
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
600 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
601
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
602 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
603
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
604
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
605 return(res_variablesSelect)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
606
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
607
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
608 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
609
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
610 # La fonction varAnnotation_gene_7blocks permet de fournir des informations sur les variables
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
611 # sélectionnées pour un design.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
612
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
613 varAnnotation_gene_7blocks <-function(variablesSelect,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
614 data_transcripto_col,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
615 data_transcripto_tae,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
616 annot_metageno_caecum,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
617 metavar_metaboLC_S1,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
618 metavar_resBio,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
619 metavar_cyto)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
620 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
621 res_variablesSelect = variablesSelect
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
622 noms_blocks = names(variablesSelect)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
623
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
624 ind_transcripto_col = which(noms_blocks == "transcripto_col")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
625
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
626 if(length(ind_transcripto_col) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
627 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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parents:
diff changeset
628
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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parents:
diff changeset
629 varSelect_transcripto_colTemp = variablesSelect[[ind_transcripto_col]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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parents:
diff changeset
630
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
631 if(length(varSelect_transcripto_colTemp) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
632 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
633 varSelect_transcripto_col = sapply(1:length(varSelect_transcripto_colTemp), FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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diff changeset
634 variable_i = varSelect_transcripto_colTemp[i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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diff changeset
635 res = gsub("Colon_", "", variable_i, fixed = TRUE)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
636
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
637 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
638 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
639
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
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diff changeset
640 dataframe_varSelect_transcripto_col = data.frame(GeneName = varSelect_transcripto_col)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
641
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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parents:
diff changeset
642 dataframe_annot_transcripto_col = data.frame(ProbeName = data_transcripto_col$genes$ProbeName,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
643 GeneName = data_transcripto_col$genes$GeneName,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
644 Description = data_transcripto_col$genes$Description,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
645 SystematicName = data_transcripto_col$genes$SystematicName)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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diff changeset
646
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
647 tab_transcripto_col = join(x = dataframe_varSelect_transcripto_col, y = dataframe_annot_transcripto_col,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
648 type = "inner",
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
649 by = "GeneName")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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diff changeset
650
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
651 res_variablesSelect[[ind_transcripto_col]] = tab_transcripto_col
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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diff changeset
652
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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parents:
diff changeset
653 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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diff changeset
654 res_variablesSelect[[ind_transcripto_col]] = ""
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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parents:
diff changeset
655
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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diff changeset
656 }
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diff changeset
657
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diff changeset
658
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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diff changeset
659
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diff changeset
660
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diff changeset
661 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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diff changeset
662
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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diff changeset
663 ind_transcripto_tae = which(noms_blocks == "transcripto_tae")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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parents:
diff changeset
664
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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diff changeset
665 if(length(ind_transcripto_tae) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
666 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
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diff changeset
667
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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diff changeset
668 varSelect_transcripto_taeTemp = variablesSelect[[ind_transcripto_tae]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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parents:
diff changeset
669
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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diff changeset
670 if(length(varSelect_transcripto_taeTemp) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
671 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
672 varSelect_transcripto_tae = sapply(1:length(varSelect_transcripto_taeTemp), FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
673 variable_i = varSelect_transcripto_taeTemp[i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
674 res = gsub("TAE_", "", variable_i, fixed = TRUE)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
675
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
676 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
677 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
678
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
679 dataframe_varSelect_transcripto_tae = data.frame(GeneName = varSelect_transcripto_tae)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
680
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
681 dataframe_annot_transcripto_tae = data.frame(ProbeName = data_transcripto_tae$genes$ProbeName,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
682 GeneName = data_transcripto_tae$genes$GeneName,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
683 Description = data_transcripto_tae$genes$Description,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
684 SystematicName = data_transcripto_tae$genes$SystematicName)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
685
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
686 tab_transcripto_tae = join(x = dataframe_varSelect_transcripto_tae, y = dataframe_annot_transcripto_tae,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
687 type = "inner",
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
688 by = "GeneName")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
689
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
690 res_variablesSelect[[ind_transcripto_tae]] = tab_transcripto_tae
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
691
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
692 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
693 res_variablesSelect[[ind_transcripto_tae]] = ""
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
694
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
695
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
696 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
697
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
698
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
699
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
700
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
701 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
702
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
703
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
704 ind_metageno_caecum = which(noms_blocks == "metageno_caecum")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
705
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
706 if(length(ind_metageno_caecum) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
707 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
708 varSelect_metageno_caecum_Temp1 = variablesSelect[[ind_metageno_caecum]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
709
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
710 if(length(varSelect_metageno_caecum_Temp1) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
711 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
712 varSelect_metageno_caecum_Temp2 = sapply(1:length(varSelect_metageno_caecum_Temp1), FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
713 ch = strsplit(varSelect_metageno_caecum_Temp1[i], split = "")[[1]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
714
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
715 if(ch[1] == "X")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
716 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
717 res = paste(ch[2:length(ch)], collapse = "")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
718
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
719 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
720 res = varSelect_metageno_caecum_Temp1[i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
721
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
722 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
723
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
724 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
725 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
726
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
727
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
728 dataframe_varSelect_metageno_caecum = data.frame(taxon = varSelect_metageno_caecum_Temp2)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
729
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
730 dataframe_annot_metageno_caecum = data.frame(annot_metageno_caecum)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
731 colnames(dataframe_annot_metageno_caecum)[1] = "taxon"
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
732
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
733 tab_metageno_caecum = join(x = dataframe_varSelect_metageno_caecum, y = dataframe_annot_metageno_caecum,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
734 type = "inner",
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
735 by = "taxon")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
736
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
737 res_variablesSelect[[ind_metageno_caecum]] = tab_metageno_caecum
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
738
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
739 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
740 res_variablesSelect[[ind_metageno_caecum]] = ""
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
741
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
742
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
743 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
744
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
745
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
746
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
747
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
748 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
749
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
750 ind_metaboLC_S1 = which(noms_blocks == "metaboLC_S1")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
751
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
752 if(length(ind_metaboLC_S1) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
753 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
754 if(length(variablesSelect[[ind_metaboLC_S1]]) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
755 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
756
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
757 dataframe_varSelect_metaboLC_S1 = data.frame(Variable = variablesSelect[[ind_metaboLC_S1]])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
758 dataframe_metavar_metaboLC_S1 = data.frame(metavar_metaboLC_S1)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
759
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
760
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
761 dataframe_metavar_varSelect_metaboLC_S1 = join(x = dataframe_varSelect_metaboLC_S1, y = dataframe_metavar_metaboLC_S1,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
762 type = "inner",
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
763 by = "Variable")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
764
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
765 res_variablesSelect[[ind_metaboLC_S1]] = dataframe_metavar_varSelect_metaboLC_S1
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
766
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
767 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
768 res_variablesSelect[[ind_metaboLC_S1]] = ""
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
769
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
770 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
771
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
772 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
773
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
774 ind_metaboGC_S1 = which(noms_blocks == "metaboGC_S1")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
775
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
776 if(length(ind_metaboGC_S1) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
777 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
778 if(length(variablesSelect[[ind_metaboGC_S1]]) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
779 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
780 res_variablesSelect[[ind_metaboGC_S1]] = data.frame(Variable = variablesSelect[[ind_metaboGC_S1]])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
781
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
782 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
783 res_variablesSelect[[ind_metaboGC_S1]] = ""
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
784
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
785 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
786
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
787
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
788 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
789
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
790 ind_resBio = which(noms_blocks == "resBio")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
791
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
792 if(length(ind_resBio) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
793 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
794 if(length(variablesSelect[[ind_resBio]]) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
795 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
796
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
797 dataframe_varSelect_resBio = data.frame(Variable = variablesSelect[[ind_resBio]])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
798 dataframe_metavar_resBio = data.frame(metavar_resBio)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
799
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
800
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
801 dataframe_metavar_varSelect_resBio = join(x = dataframe_varSelect_resBio, y = dataframe_metavar_resBio,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
802 type = "inner",
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
803 by = "Variable")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
804
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
805 res_variablesSelect[[ind_resBio]] = dataframe_metavar_varSelect_resBio
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
806
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
807 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
808 res_variablesSelect[[ind_resBio]] = ""
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
809
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
810 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
811
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
812 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
813
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
814 ind_cyto = which(noms_blocks == "cyto")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
815
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
816 if(length(ind_cyto) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
817 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
818 if(length(variablesSelect[[ind_cyto]]) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
819 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
820
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
821 dataframe_varSelect_cyto = data.frame(Variable = variablesSelect[[ind_cyto]])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
822 dataframe_metavar_cyto = data.frame(metavar_cyto)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
823
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
824
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
825 dataframe_metavar_varSelect_cyto = join(x = dataframe_varSelect_cyto, y = dataframe_metavar_cyto,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
826 type = "inner",
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
827 by = "Variable")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
828
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
829 res_variablesSelect[[ind_cyto]] = dataframe_metavar_varSelect_cyto
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
830
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
831 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
832 res_variablesSelect[[ind_cyto]] = ""
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
833
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
834 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
835
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
836 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
837
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
838
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
839 return(res_variablesSelect)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
840
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
841
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
842 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
843
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
844
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
845
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
846 # Integration 6 blocs norm sonde ------------------------------------------
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
847
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
848 # La fonction plotVarZoom permet de zoomer sur le cercle de corrélation et de récupérer les variables
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
849 # contenues dans ce rectangle.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
850
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
851 plotVarZoom <-function(res_block_splsda,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
852 comp = 1:2,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
853 blocks,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
854 block_Y = NULL,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
855 vec_col,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
856 cutoff,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
857 rad.in = 0.5,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
858 min.X = -1,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
859 max.X = 1,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
860 min.Y = -1,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
861 max.Y = 1,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
862 cex = 0.7,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
863 cex_legend = 0.8,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
864 pos = c(1.2, 0),
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
865 pch = 20,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
866 inset = c(-0.25, 0))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
867 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
868 if(class(res_block_splsda)[1] == "block.splsda")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
869 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
870 circle = list()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
871 circle[[1]] = ellipse(0, levels = 1, t = 1)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
872 circle[[2]] = ellipse(0, levels = 1, t = rad.in)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
873 circle = data.frame(do.call("rbind", circle), "Circle" = c(rep("Main circle", 100), rep("Inner circle", 100)))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
874
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
875 MainCircle = circle[grep("Main circle", circle[, 3]), ]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
876 InnerCircle = circle[grep("Inner circle", circle[, 3]), ]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
877
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
878
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
879 if(length(blocks) > 1)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
880 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
881 noms_bloc = names(res_block_splsda$variates)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
882 mat_comp1 = sapply(blocks, FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
883 res = res_block_splsda$variates[[i]][, 1]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
884
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
885 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
886 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
887
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
888 colnames(mat_comp1) = noms_bloc[blocks]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
889 mat_cor_comp1 = cor(mat_comp1)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
890
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
891
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
892 mat_comp2 = sapply(blocks, FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
893 res = res_block_splsda$variates[[i]][, 2]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
894
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
895 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
896 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
897
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
898 colnames(mat_comp2) = noms_bloc[blocks]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
899 mat_cor_comp2 = cor(mat_comp2)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
900
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
901 } # Fin if(length(blocks) > 1).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
902
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
903 # Pour chaque bloc, calcul des corrélations entre la première
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
904 # composante et les variables sélectionnées et les corrélations entre
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
905 # la deuxième composante et les variables sélectionnées. Pour la réponse,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
906 # calcul de la corrélation entre les variables de la réponse et la première composante
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
907 # du premier bloc sélectionné et de la corrélation entre les variables de
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
908 # la réponse et la deuxième composante du premier bloc sélectionné.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
909
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
910 liste_matCor_comp_var = list()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
911
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
912 varSelect_comp1 = selectVar(res_block_splsda,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
913 comp = comp[1])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
914
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
915 varSelect_comp2 = selectVar(res_block_splsda,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
916 comp = comp[2])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
917
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
918 vec_nom_blockEtReponse = c()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
919 blocksEtReponse = c(blocks, which(res_block_splsda$names$blocks == "Y"))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
920
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
921 for(i in 1:length(blocksEtReponse))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
922 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
923 indice_block_i = blocksEtReponse[i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
924 nom_blockEtReponse_i = res_block_splsda$names$blocks[indice_block_i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
925
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
926 if(nom_blockEtReponse_i == "Y")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
927 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
928 if(!is.null(block_Y))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
929 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
930 block_i = block_Y
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
931
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
932 comp1 = res_block_splsda$variates[[blocks[1]]][, comp[1]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
933 comp2 = res_block_splsda$variates[[blocks[1]]][, comp[2]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
934
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
935 vecCor_comp1_var = sapply(1:dim(block_i)[2], FUN = function(j){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
936 cor(comp1, block_i[, j], use = "complete.obs")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
937 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
938
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
939 vecCor_comp2_var = sapply(1:dim(block_i)[2], FUN = function(j){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
940 cor(comp2, block_i[, j], use = "complete.obs")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
941
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
942 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
943
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
944
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
945 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
946 cat("La réponse n'est pas saisie comme paramètre d'entrée", "\n")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
947
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
948 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
949
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
950
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
951
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
952 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
953 comp1 = res_block_splsda$variates[[indice_block_i]][, comp[1]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
954 comp2 = res_block_splsda$variates[[indice_block_i]][, comp[2]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
955
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
956 varSelect_comp1_i = varSelect_comp1[[indice_block_i]][[1]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
957 varSelect_comp2_i = varSelect_comp2[[indice_block_i]][[1]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
958 varSelect_i = unique(c(varSelect_comp1_i, varSelect_comp2_i))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
959
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
960 block_i = res_block_splsda$X[[indice_block_i]][, varSelect_i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
961
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
962 if(i == 1)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
963 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
964 vecCor_comp1_var = sapply(1:dim(block_i)[2], FUN = function(j){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
965 cor(comp1, block_i[, j], use = "complete.obs")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
966 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
967
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
968 vecCor_comp2_var = sapply(1:dim(block_i)[2], FUN = function(j){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
969 cor(comp2, block_i[, j], use = "complete.obs")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
970 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
971
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
972 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
973 signeCor_comp1 = sign(mat_cor_comp1[1, indice_block_i])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
974
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
975 vecCor_comp1_var = sapply(1:dim(block_i)[2], FUN = function(j){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
976 res = signeCor_comp1*cor(comp1, block_i[, j], use = "complete.obs")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
977
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
978 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
979 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
980
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
981 signeCor_comp2 = sign(mat_cor_comp2[1, indice_block_i])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
982
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
983 vecCor_comp2_var = sapply(1:dim(block_i)[2], FUN = function(j){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
984 res = signeCor_comp2*cor(comp2, block_i[, j], use = "complete.obs")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
985
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
986 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
987 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
988
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
989 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
990
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
991
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
992 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
993
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
994 matCor_comp_var = rbind(vecCor_comp1_var,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
995 vecCor_comp2_var)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
996
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
997 colnames(matCor_comp_var) = colnames(block_i)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
998
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
999
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1000 liste_matCor_comp_var[[i]] = matCor_comp_var
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1001
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1002 vec_nom_blockEtReponse_i = rep(nom_blockEtReponse_i, dim(block_i)[2])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1003 vec_nom_blockEtReponse = c(vec_nom_blockEtReponse, vec_nom_blockEtReponse_i)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1004
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1005 } # Fin for(i in 1:length(blocks)).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1006
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1007
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1008 matCor_Allcomp_Allvar = t(Reduce(cbind, liste_matCor_comp_var))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1009
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1010 # indice permet de récupérer les variables de chaque bloc fortement corrélées avec soit
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1011 # la première composante ou la deuxième composante dans une partie du cercle de corrélation
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1012 # et de récupérer la variable réponse dans une partie du cercle de corrélation.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1013
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1014 indice = sapply(1:dim(matCor_Allcomp_Allvar)[1], FUN = function(k){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1015 cor1 = matCor_Allcomp_Allvar[k, 1]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1016 cor2 = matCor_Allcomp_Allvar[k, 2]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1017 blockEtReponse_k = vec_nom_blockEtReponse[k]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1018
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1019 if(blockEtReponse_k == "Y")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1020 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1021 cond2 = cor1 > min.X & cor1 < max.X & cor2 > min.Y & cor2 < max.Y
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1022
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1023 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1024 cond1 = abs(cor1) > cutoff | abs(cor2) > cutoff
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1025
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1026 cond2 = cor1 > min.X & cor1 < max.X & cor2 > min.Y & cor2 < max.Y & cond1
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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parents:
diff changeset
1027
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1028 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1029
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1030
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1031 return(cond2)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1032 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1033
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1034 matCor_Allcomp_AllvarSelect = matCor_Allcomp_Allvar[indice, , drop = FALSE]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1035 varSelect = rownames(matCor_Allcomp_AllvarSelect)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1036
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1037 dataframe_Cor_Allcomp_Allvar = data.frame(cbind(rownames(matCor_Allcomp_Allvar),
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1038 vec_nom_blockEtReponse,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1039 matCor_Allcomp_Allvar))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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parents:
diff changeset
1040
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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parents:
diff changeset
1041 colnames(dataframe_Cor_Allcomp_Allvar) = c("variable",
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1042 "bloc",
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1043 "cor_comp1_var",
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1044 "cor_comp2_var")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1045
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1046 dataframe_Cor_Allcomp_Allvar[, 1:2] = apply(dataframe_Cor_Allcomp_Allvar[, 1:2], 2, as.character)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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parents:
diff changeset
1047
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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parents:
diff changeset
1048 dataframe_Cor_Allcomp_AllvarSelect = dataframe_Cor_Allcomp_Allvar[indice, ]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1049
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1050
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1051 # Tracé de la superposition des cerles de corrélation.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1052
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1053 plot(MainCircle[, 1], MainCircle[, 2],
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1054 type = "l",
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1055 xlab = paste0("composante ", comp[1]),
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1056 ylab = paste0("composante ", comp[2]))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1057
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1058 points(InnerCircle[, 1], InnerCircle[, 2],
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1059 type = "l")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1060
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1061 if(dim(matCor_Allcomp_AllvarSelect)[1] != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1062 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1063
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1064 nom_blockEtReponseSelect = unique(dataframe_Cor_Allcomp_AllvarSelect[, 2])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1065 indice_blockEtReponseSelect = sapply(1:length(nom_blockEtReponseSelect), FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1066 ind = which(res_block_splsda$names$blocks == nom_blockEtReponseSelect[i])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1067
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1068 if(length(ind) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1069 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1070 res = ind
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1071
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1072 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1073 res = which(res_block_splsda$names$blocks == "Y")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1074
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1075 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1076
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1077 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1078 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1079 vec_colSelect = vec_col[indice_blockEtReponseSelect]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1080
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1081 if(length(blocksEtReponse) == 1)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1082 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1083 points(matCor_Allcomp_AllvarSelect[, 1], matCor_Allcomp_AllvarSelect[, 2],
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1084 col = NULL)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1085
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1086 text(matCor_Allcomp_AllvarSelect[, 1], matCor_Allcomp_AllvarSelect[, 2],
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1087 labels = rownames(matCor_Allcomp_AllvarSelect),
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1088 cex = cex,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1089 col = vec_colSelect[1])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1090
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1091 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1092
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1093 nbVarSelect_bloc = cumsum(sapply(1:length(nom_blockEtReponseSelect), FUN = function(j){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1094 res = length(which(dataframe_Cor_Allcomp_AllvarSelect[, 2] == nom_blockEtReponseSelect[j]))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1095
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1096 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1097 }))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1098
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1099 for(i in 1:length(nbVarSelect_bloc))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1100 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1101 if(i == 1)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1102 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1103 indice1 = 1:nbVarSelect_bloc[1]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1104
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1105 if(length(indice1) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1106 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1107 matCor_Allcomp_AllvarSelect2 = matCor_Allcomp_AllvarSelect[indice1, , drop = FALSE]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1108
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1109 points(matCor_Allcomp_AllvarSelect2[, 1], matCor_Allcomp_AllvarSelect2[, 2],
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1110 col = NULL)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1111
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1112 text(matCor_Allcomp_AllvarSelect2[, 1], matCor_Allcomp_AllvarSelect2[, 2],
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1113 labels = rownames(matCor_Allcomp_AllvarSelect2),
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1114 cex = cex,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1115 col = rep(vec_colSelect[i], dim(matCor_Allcomp_AllvarSelect2)[1]))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1116
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1117 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1118 cat(paste0("Il n'y a de variables dans cette zone du cercle de corrélation pour le bloc ", nom_blockEtReponseSelect[i]), "\n")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1119
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1120
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1121 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1122
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1123
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1124 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1125 indice2 = (nbVarSelect_bloc[i - 1] + 1):nbVarSelect_bloc[i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1126
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1127 if(length(indice2) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1128 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1129 matCor_Allcomp_AllvarSelect2 = matCor_Allcomp_AllvarSelect[indice2, , drop = FALSE]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1130
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1131 points(matCor_Allcomp_AllvarSelect2[, 1], matCor_Allcomp_AllvarSelect2[, 2],
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1132 col = NULL)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1133
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1134 text(matCor_Allcomp_AllvarSelect2[, 1], matCor_Allcomp_AllvarSelect2[, 2],
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1135 labels = rownames(matCor_Allcomp_AllvarSelect2),
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1136 cex = cex,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1137 col = rep(vec_colSelect[i], dim(matCor_Allcomp_AllvarSelect2)[1]))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1138
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1139
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1140 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1141 cat(paste0("Il n'y a de variables dans cette zone du cercle de corrélation pour le bloc ", nom_blockEtReponseSelect[i]), "\n")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1142
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ppericard
parents:
diff changeset
1143 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1144
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1145
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1146 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1147
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1148 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1149
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1150 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1151
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1152 par(xpd = TRUE)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1153 legend(x = pos[1], y = pos[2],
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1154 legend = nom_blockEtReponseSelect,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1155 pch = pch,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1156 col = vec_colSelect,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1157 cex = cex_legend,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1158 inset = inset)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1159
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1160
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1161 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1162 cat("Il n'y a de variables dans cette zone du cercle de corrélation", "\n")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1163
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1164 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1165
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1166
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1167 # Suppression de dataframe_Cor_Allcomp_Allvar, dataframe_Cor_Allcomp_AllvarSelect et varSelect de la variable
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1168 # réponse.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1169
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1170 if(!is.null(block_Y))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1171 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1172 for(i in 1:dim(block_Y)[2])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1173 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1174 variableReponse = colnames(block_Y)[i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1175
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1176 # dataframe_Cor_Allcomp_Allvar
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1177 if(dim(dataframe_Cor_Allcomp_Allvar)[1] != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1178 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1179 ind_Allvar = which(dataframe_Cor_Allcomp_Allvar$variable == variableReponse)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1180
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1181 if(length(ind_Allvar) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1182 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1183 dataframe_Cor_Allcomp_Allvar = dataframe_Cor_Allcomp_Allvar[- ind_Allvar, ]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1184
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1185 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1186
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1187 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1188
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1189 # dataframe_Cor_Allcomp_AllvarSelect
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1190 if(dim(dataframe_Cor_Allcomp_AllvarSelect)[1] != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1191 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1192 ind_AllvarSelect = which(dataframe_Cor_Allcomp_AllvarSelect$variable == variableReponse)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1193
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1194 if(length(ind_AllvarSelect) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1195 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1196 dataframe_Cor_Allcomp_AllvarSelect = dataframe_Cor_Allcomp_AllvarSelect[- ind_AllvarSelect, ]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1197
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1198 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1199
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1200 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1201
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1202 # varSelect
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1203 if(length(varSelect) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1204 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1205 ind_varSelect = which(varSelect == variableReponse)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1206
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1207 if(length(ind_varSelect) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1208 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1209 varSelect = varSelect[- ind_varSelect]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1210
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1211 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1212
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1213 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1214
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
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parents:
diff changeset
1215
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1216
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1217 } # Fin for(i in 1:dim(block_Y)[2]).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1218
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1219 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1220
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1221
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1222 res = list(dataframe_Cor_Allcomp_Allvar = dataframe_Cor_Allcomp_Allvar,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1223 dataframe_Cor_Allcomp_AllvarSelect = dataframe_Cor_Allcomp_AllvarSelect,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1224 varSelect = varSelect)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1225
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1226 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1227
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1228 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1229 cat("Erreur : il ne s'agit pas de la sortie de la fonction block.splsda", "\n")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1230
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1231 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1232
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1233 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1234
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1235
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ppericard
parents:
diff changeset
1236 # La fonction networkVarSelect permet de tracer un réseau pour les variables de
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1237 # certains blocs.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1238
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1239 networkVarSelect <-function(object,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1240 mat_Y,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1241 comp = 1:2,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1242 listeVar,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1243 blocks,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1244 cutoff = 0
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1245 )
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1246 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1247
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1248 if(class(object)[1] == "block.splsda")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1249 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1250 nomBlocs = names(listeVar)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1251
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1252 liste_XSelect = lapply(1:length(listeVar), FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1253 nomBloc_i = names(listeVar)[i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1254 ind1 = which(object$names$blocks == nomBloc_i)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1255 ind2 = colnames(object$X[[ind1]])%in%listeVar[[i]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1256 res = object$X[[ind1]][, ind2, drop = FALSE]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1257
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1258 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1259 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1260 names(liste_XSelect) = nomBlocs
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1261
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1262 liste_matSelect = liste_XSelect
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1263
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1264 if(!is.null(mat_Y))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1265 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1266 liste_matSelect = c(liste_matSelect, list(mat_Y))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1267 names(liste_matSelect)[length(liste_matSelect)] = "Y"
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1268
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1269 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1270
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1271 # compute the similarity between var1 of block1 and var2 of block2.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1272 coord = list()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1273
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1274 for(k in 1:length(blocks))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1275 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1276 nomBloc_k = names(liste_matSelect)[k]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1277 mat_k = liste_matSelect[[k]][, ,drop = FALSE]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1278
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1279 if(nomBloc_k == "Y")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1280 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1281 coord[[k]] = cor(mat_k, object$variates[[blocks[1]]][, comp])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1282
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1283
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1284
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1285 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1286 coord[[k]] = cor(mat_k, object$variates[[blocks[k]]][, comp])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1287
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1288
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1289 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1290
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1291 if(dim(mat_k)[2] == 1)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1292 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1293 coord[[k]] = as.matrix(coord[[k]],
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1294 nrow = 1)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1295 rownames(coord[[k]]) = colnames(mat_k)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1296
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1297 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1298
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1299 } # Fin for(k in 1:length(blocks)).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1300
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1301 l = 1
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1302 M_block = list()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1303 node.X1 = node.X2 = w = NULL
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1304
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1305
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1306 for(j in 1:(length(blocks) - 1))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1307 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1308 for(k in (j + 1):length(blocks))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1309 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1310 M_block[[l]] = coord[[j]][, comp, drop = FALSE] %*% t(coord[[k]][, comp, drop = FALSE])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1311
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1312 X1 = rownames(coord[[j]])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1313 X2 = rownames(coord[[k]])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1314
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1315 rep.X1 = rep(X1, each = length(X2))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1316 rep.X2 = rep(X2, length(X1))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1317
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1318 node.X1= c(node.X1, rep.X1)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1319 node.X2 = c(node.X2, rep.X2)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1320
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1321 w = c(w, as.vector(t(M_block[[l]])))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1322
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1323 l = l + 1
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1324
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1325 } # Fin for(k in (j + 1):length(blocks)).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1326
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1327 } # Fin for(j in 1:(length(blocks) - 1)).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1328
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1329 # nodes
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1330 group = NULL
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1331 temp = lapply(liste_matSelect, function(x) colnames(x))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1332
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1333 for (i in 1:length(temp))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1334 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1335 group = c(group, rep(names(temp)[i], length(temp[[i]])))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1336
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1337 } # Fin for (i in 1:length(temp)).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1338
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1339 # nodes
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1340 nodes = data.frame(name = unlist(temp),
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1341 group = group)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1342
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1343 # gR
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1344 relations = data.frame(from = node.X1,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1345 to = node.X2,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1346 weight = w)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1347
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1348 idx = (abs(w) >= cutoff)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1349 relations = relations[idx, , drop = FALSE]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1350
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1351 gR = graph.data.frame(relations,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1352 directed = FALSE,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1353 vertices = nodes)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1354
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1355
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1356 block.var.names = sapply(1:length(liste_matSelect), FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1357 res = colnames(liste_matSelect[[i]])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1358
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1359 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1360 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1361 V(gR)$label = unlist(block.var.names)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1362
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1363 gR = delete.vertices(gR, which(degree(gR) == 0))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1364
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1365
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1366 res = list(gR = gR)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1367
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1368 l = 1
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1369 for (i in 1:(length(blocks)-1))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1370 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1371 for (j in (i + 1):length(blocks))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1372 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1373 res[paste("M", names(liste_matSelect)[i], names(liste_matSelect)[j], sep="_")] = list(M_block[[l]])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1374 l = l + 1
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1375
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1376 } # Fin for (j in (i + 1):length(blocks)).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1377
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1378 } # Fin for (i in 1:(length(blocks)-1).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1379
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1380 res$cutoff = cutoff
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1381
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1382 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1383
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1384 } # Fin if(class(object)[1] == "block.splsda").
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1385
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1386
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1387
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1388 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1389
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1390 # La fonction varAnnotation_6blocks permet de fournir des informations sur les variables
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1391 # sélectionnées pour un design.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1392
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1393 varAnnotation_6blocks <-function(variablesSelect,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1394 data_transcripto_col,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1395 data_transcripto_tae,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1396 annot_metageno_caecum)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1397 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1398 res_variablesSelect = variablesSelect
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1399 noms_blocks = names(variablesSelect)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1400
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1401 ind_transcripto_col = which(noms_blocks == "transcripto_col")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1402
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1403 if(length(variablesSelect[[ind_transcripto_col]]) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1404 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1405
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1406 varSelect_transcripto_colTemp = variablesSelect[[ind_transcripto_col]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1407 varSelect_transcripto_col = sapply(1:length(varSelect_transcripto_colTemp), FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1408 ch = strsplit(varSelect_transcripto_colTemp[i], split = "_")[[1]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1409
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1410 res = paste(ch[2:length(ch)], collapse = "_")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1411
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1412 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1413 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1414
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1415 dataframe_varSelect_transcripto_col = data.frame(ProbeName = varSelect_transcripto_col)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1416
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1417 dataframe_annot_transcripto_col = data.frame(ProbeName = data_transcripto_col$genes$ProbeName,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1418 GeneName = data_transcripto_col$genes$GeneName,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1419 Description = data_transcripto_col$genes$Description,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1420 SystematicName = data_transcripto_col$genes$SystematicName)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1421
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1422 tab_transcripto_col = join(x = dataframe_varSelect_transcripto_col, y = dataframe_annot_transcripto_col,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1423 type = "inner",
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1424 by = "ProbeName")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1425
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1426 res_variablesSelect[[ind_transcripto_col]] = tab_transcripto_col
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1427
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1428
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1429 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1430
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1431 ind_transcripto_tae = which(noms_blocks == "transcripto_tae")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1432
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1433 if(length(variablesSelect[[ind_transcripto_tae]]) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1434 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1435 varSelect_transcripto_taeTemp = variablesSelect[[ind_transcripto_tae]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1436 varSelect_transcripto_tae = sapply(1:length(varSelect_transcripto_taeTemp), FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1437 ch = strsplit(varSelect_transcripto_taeTemp[i], split = "_")[[1]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1438
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1439 res = paste(ch[2:length(ch)], collapse = "_")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1440
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1441 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1442 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1443
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1444 dataframe_varSelect_transcripto_tae = data.frame(ProbeName = varSelect_transcripto_tae)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1445
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1446 dataframe_annot_transcripto_tae = data.frame(ProbeName = data_transcripto_tae$genes$ProbeName,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1447 GeneName = data_transcripto_tae$genes$GeneName,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1448 Description = data_transcripto_tae$genes$Description,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1449 SystematicName = data_transcripto_tae$genes$SystematicName)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1450
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1451 tab_transcripto_tae = join(x = dataframe_varSelect_transcripto_tae, y = dataframe_annot_transcripto_tae,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1452 type = "inner",
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1453 by = "ProbeName")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1454
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1455 res_variablesSelect[[ind_transcripto_tae]] = tab_transcripto_tae
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1456
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1457 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1458
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1459
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1460 ind_metageno_caecum = which(noms_blocks == "metageno_caecum")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1461
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1462 if(length(variablesSelect[[ind_metageno_caecum]]) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1463 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1464 varSelect_metageno_caecum_Temp1 = variablesSelect[[ind_metageno_caecum]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1465 varSelect_metageno_caecum_Temp2 = sapply(1:length(varSelect_metageno_caecum_Temp1), FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1466 ch = strsplit(varSelect_metageno_caecum_Temp1[i], split = "")[[1]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1467
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1468 if(ch[1] == "X")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1469 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1470 res = paste(ch[2:length(ch)], collapse = "")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1471
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1472 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1473 res = varSelect_metageno_caecum_Temp1[i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1474
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1475 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1476
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1477 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1478 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1479
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1480
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1481 dataframe_varSelect_metageno_caecum = data.frame(taxon = varSelect_metageno_caecum_Temp2)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1482
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1483 dataframe_annot_metageno_caecum = data.frame(annot_metageno_caecum)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1484 colnames(dataframe_annot_metageno_caecum)[1] = "taxon"
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1485
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1486 tab_metageno_caecum = join(x = dataframe_varSelect_metageno_caecum, y = dataframe_annot_metageno_caecum,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1487 type = "inner",
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1488 by = "taxon")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1489
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1490 res_variablesSelect[[ind_metageno_caecum]] = tab_metageno_caecum
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1491
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1492
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1493 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1494
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1495 ind_metaboLC_S1 = which(noms_blocks == "metaboLC_S1")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1496
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1497 if(length(variablesSelect[[ind_metaboLC_S1]]) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1498 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1499 res_variablesSelect[[ind_metaboLC_S1]] = data.frame(variable = variablesSelect[[ind_metaboLC_S1]])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1500
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1501 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1502
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1503 ind_resBio = which(noms_blocks == "resBio")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1504
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1505 if(length(variablesSelect[[ind_resBio]]) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1506 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1507 res_variablesSelect[[ind_resBio]] = data.frame(variable = variablesSelect[[ind_resBio]])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1508
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1509 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1510
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1511 ind_cyto = which(noms_blocks == "cyto")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1512
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1513 if(length(variablesSelect[[ind_cyto]]) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1514 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1515 res_variablesSelect[[ind_cyto]] = data.frame(variable = variablesSelect[[ind_cyto]])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1516
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1517 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1518
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1519
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1520 return(res_variablesSelect)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1521
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1522
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1523 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1524
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1525
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1526
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1527 # Integration 6 blocs norm gene -------------------------------------------
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1528
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1529
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1530 # La fonction matriceCorrelation_comp calcule la matrice de corrélation entre les comp[1]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1531 # composantes de chaque bloc et la matrice de corrélation entre les comp[2] composantes de
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1532 # chaque bloc.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1533
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1534 matriceCorrelation_comp <-function(res_block_splsda,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1535 comp = 1:2)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1536 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1537 vec_blocksTemp = res_block_splsda$names$blocks
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1538 ind_Y = which(vec_blocksTemp == "Y")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1539 vec_blocks = vec_blocksTemp[- ind_Y]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1540 vec_indice_blocks = sapply(1:length(vec_blocks), FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1541 res = which(res_block_splsda$names$blocks == vec_blocks[i])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1542
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1543 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1544 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1545
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1546 # Calcul de la matrice de corrélations entre les comp[1] composantes de chaque bloc
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1547 # et de la matrice de corrélation entre les comp[2] composantes de chaque bloc.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1548
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1549 mat_comp1 = sapply(1:length(vec_indice_blocks), FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1550 res = res_block_splsda$variates[[vec_indice_blocks[i]]][, comp[1]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1551
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1552 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1553 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1554
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1555 colnames(mat_comp1) = vec_blocks
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1556 mat_cor_comp1 = cor(mat_comp1)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1557
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1558 mat_comp2 = sapply(1:length(vec_indice_blocks), FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1559 res = res_block_splsda$variates[[vec_indice_blocks[i]]][, comp[2]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1560
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1561 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1562 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1563
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1564 colnames(mat_comp2) = vec_blocks
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1565 mat_cor_comp2 = cor(mat_comp2)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1566
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1567 return(list(mat_cor_comp1 = mat_cor_comp1,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1568 mat_cor_comp2 = mat_cor_comp2))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1569 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1570
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1571 # La fonction matCor détermine toutes les combinaisons possibles des blocs
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1572 # dont nous pouvons superposer les cercles de corrélation. Cette fonction calcule,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1573 # pour chaque variable (variable d'un bloc ou une variable réponse), la corrélation de
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1574 # cette variable avec la première composante et la corrélation de cette variable avec la
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1575 # deuxième composante.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1576
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1577
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1578 matCor <-function(res_block_splsda,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1579 mat_cor_comp1,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1580 mat_cor_comp2,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1581 block_Y,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1582 comp = 1:2,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1583 cutoff_comp)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1584 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1585
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1586 noms_blocTemp = res_block_splsda$names$blocks
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1587 ind_Y = which(noms_blocTemp == "Y")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1588 noms_bloc = noms_blocTemp[- ind_Y]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1589
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1590 # Détermination de toutes les combinaisons possibles de blocs dont nous pouvons superposer
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1591 # les cercles de corrélation.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1592
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1593 blockSelect = unique(lapply(1:dim(mat_cor_comp1)[1], FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1594 col_mat_cor_comp1_i = mat_cor_comp1[, i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1595 col_mat_cor_comp2_i = mat_cor_comp2[, i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1596
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1597 resultat = c()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1598
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1599 for(j in 1:length(col_mat_cor_comp1_i))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1600 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1601 cond = abs(col_mat_cor_comp1_i[j]) > cutoff_comp & abs(col_mat_cor_comp2_i[j]) > cutoff_comp
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1602
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1603 if(cond)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1604 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1605 resultat = c(resultat, j)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1606
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1607 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1608
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1609 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1610
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1611 return(resultat)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1612
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1613 }))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1614
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1615
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1616 liste_noms_blocks = list()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1617
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1618 for(i in 1:length(blockSelect))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1619 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1620 blockSelect_i = blockSelect[[i]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1621
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1622 for(k in 1:length(blockSelect_i))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1623 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1624 matComb = combn(blockSelect_i, m = k)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1625
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1626 res = lapply(1:dim(matComb)[2], FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1627 comb_i = matComb[, i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1628 resultat = noms_bloc[comb_i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1629
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1630 return(resultat)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1631 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1632
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1633 for(j in 1:length(res))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1634 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1635 liste_noms_blocks = c(liste_noms_blocks, list(res[[j]]))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1636
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1637 } # Fin for(j in 1:length(liste_noms_blocks)).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1638
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1639
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1640 } # Fin for(k in 1:length(blockSelect_i)).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1641
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1642 } # Fin for(i in 1:length(blockSelect)).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1643
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1644 liste_noms_blocks = unique(liste_noms_blocks)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1645
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1646 # Pour chaque bloc, calcul des corrélations entre la première
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1647 # composante et les variables sélectionnées et les corrélations entre
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1648 # la deuxième composante et les variables sélectionnées. Pour la réponse,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1649 # calcul de la corrélation entre les variables de la réponse et la première composante
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1650 # du premier bloc sélectionné et de la corrélation entre les variables de
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1651 # la réponse et la deuxième composante du premier bloc sélectionné.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1652
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1653 liste_matCor_comp_var_all = list()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1654
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1655 varSelect_comp1 = selectVar(res_block_splsda,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1656 comp = comp[1])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1657
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1658 varSelect_comp2 = selectVar(res_block_splsda,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1659 comp = comp[2])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1660
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1661 blockSelectEtReponse = list()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1662
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1663 for(i in 1:length(blockSelect))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1664 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1665 blockSelectEtReponse[[i]] = c(blockSelect[[i]], which(res_block_splsda$names$blocks == "Y"))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1666
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1667
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1668 } # Fin for(i in 1:length(blockSelect)).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1669
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1670
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1671 for(i in 1:length(blockSelectEtReponse))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1672 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1673 blockSelectEtReponse_i = blockSelectEtReponse[[i]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1674 vec_nom_blockEtReponse = c()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1675 liste_matCor_comp_var = list()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1676
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1677 for(j in 1:length(blockSelectEtReponse_i))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1678 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1679 indice_block_i_j = blockSelectEtReponse_i[j]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1680 nom_blockEtReponse_i_j = res_block_splsda$names$blocks[indice_block_i_j]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1681
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1682 if(nom_blockEtReponse_i_j == "Y")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1683 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1684 if(!is.null(block_Y))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1685 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1686 block_i_j = block_Y
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1687
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1688 comp1 = res_block_splsda$variates[[blockSelectEtReponse_i[1]]][, comp[1]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1689 comp2 = res_block_splsda$variates[[blockSelectEtReponse_i[1]]][, comp[2]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1690
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1691 vecCor_comp1_var = sapply(1:dim(block_Y)[2], FUN = function(j){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1692 cor(comp1, block_Y[, j], use = "complete.obs")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1693 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1694
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1695 vecCor_comp2_var = sapply(1:dim(block_Y)[2], FUN = function(j){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1696 cor(comp2, block_Y[, j], use = "complete.obs")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1697
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1698 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1699
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1700
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1701 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1702 cat("La réponse n'est pas saisie comme paramètre d'entrée", "\n")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1703
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1704 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1705
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1706
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1707
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1708 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1709 comp1 = res_block_splsda$variates[[indice_block_i_j]][, comp[1]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1710 comp2 = res_block_splsda$variates[[indice_block_i_j]][, comp[2]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1711
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1712 varSelect_comp1_i_j = varSelect_comp1[[indice_block_i_j]][[1]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1713 varSelect_comp2_i_j = varSelect_comp2[[indice_block_i_j]][[1]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1714 varSelect_i_j = unique(c(varSelect_comp1_i_j, varSelect_comp2_i_j))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1715
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1716 block_i_j = res_block_splsda$X[[indice_block_i_j]][, varSelect_i_j]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1717
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1718 if(i == 1)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1719 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1720 vecCor_comp1_var = sapply(1:dim(block_i_j)[2], FUN = function(j){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1721 cor(comp1, block_i_j[, j], use = "complete.obs")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1722 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1723
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1724 vecCor_comp2_var = sapply(1:dim(block_i_j)[2], FUN = function(j){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1725 cor(comp2, block_i_j[, j], use = "complete.obs")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1726 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1727
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1728 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1729 signeCor_comp1 = sign(mat_cor_comp1[1, indice_block_i_j])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1730
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1731 vecCor_comp1_var = sapply(1:dim(block_i_j)[2], FUN = function(j){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1732 res = signeCor_comp1*cor(comp1, block_i_j[, j], use = "complete.obs")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1733
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1734 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1735 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1736
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1737 signeCor_comp2 = sign(mat_cor_comp2[1, indice_block_i_j])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1738
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1739 vecCor_comp2_var = sapply(1:dim(block_i_j)[2], FUN = function(j){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1740 res = signeCor_comp2*cor(comp2, block_i_j[, j], use = "complete.obs")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1741
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1742 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1743 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1744
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1745 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1746
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1747
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1748 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1749
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1750 matCor_comp_var = rbind(vecCor_comp1_var,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1751 vecCor_comp2_var)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1752
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1753 colnames(matCor_comp_var) = colnames(block_i_j)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1754
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1755
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1756 liste_matCor_comp_var[[j]] = matCor_comp_var
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1757
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1758 vec_nom_blockEtReponse_i_j = rep(nom_blockEtReponse_i_j, dim(block_i_j)[2])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1759 vec_nom_blockEtReponse = c(vec_nom_blockEtReponse, vec_nom_blockEtReponse_i_j)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1760
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1761 } # Fin for(j in 1:length(blockSelectEtReponse_i)).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1762
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1763 matCor_Allcomp_Allvar = t(Reduce(cbind, liste_matCor_comp_var))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1764 dataframe_Cor_Allcomp_Allvar = data.frame(cbind(rownames(matCor_Allcomp_Allvar),
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1765 vec_nom_blockEtReponse,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1766 matCor_Allcomp_Allvar))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1767
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1768 colnames(dataframe_Cor_Allcomp_Allvar) = c("variable",
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1769 "bloc",
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1770 "cor_comp1_var",
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1771 "cor_comp2_var")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1772
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1773 liste_matCor_comp_var_all[[i]] = dataframe_Cor_Allcomp_Allvar
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1774
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1775
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1776 } # Fin for(i in 1:length(blocks)).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1777
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1778
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1779 names(liste_matCor_comp_var_all) = sapply(1:length(blockSelectEtReponse), FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1780 blockSelectEtReponse_i = blockSelectEtReponse[[i]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1781 blocks_i = blockSelectEtReponse_i[blockSelectEtReponse_i != ind_Y]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1782 nomsBlocks = paste(res_block_splsda$names$blocks[blocks_i], collapse = "_")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1783
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1784 return(nomsBlocks)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1785 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1786
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1787
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1788 return(list(liste_matCor_comp_var_all = liste_matCor_comp_var_all,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1789 liste_noms_blocks = liste_noms_blocks))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1790
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1791 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1792
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1793
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1794 # La fonction circleCorZoom permet superposer des cercles de corrélations et de zoomer un rectangle du cercle de corrélations.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1795 # Cette fonction permet de récupérer les variables contenues dans ce rectangle.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1796
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1797 circleCorZoom <-function(dataframe_Cor_Allcomp_Allvar,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1798 mat_cor_comp1,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1799 mat_cor_comp2,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1800 nomsBlock,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1801 comp = 1:2,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1802 cutoff = 0.85,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1803 cutoff_comp = 0.8,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1804 min.X = -1,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1805 max.X = 1,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1806 min.Y = -1,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1807 max.Y = 1,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1808 vec_col = colorRampPalette(brewer.pal(9, "Spectral"))(length(unique(dataframe_Cor_Allcomp_Allvar$bloc))),
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1809 rad.in = 0.5,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1810 cex = 0.7,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1811 cex_legend = 0.8,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1812 pos = c(1.2, 0),
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1813 pch = 20,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1814 inset = c(-0.25, 0))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1815 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1816
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1817 # Nous vérifions que nous pouvons superposer les cercles de corrélation.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1818
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1819 blockSelect = unique(lapply(1:dim(mat_cor_comp1)[1], FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1820 col_mat_cor_comp1_i = mat_cor_comp1[, i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1821 col_mat_cor_comp2_i = mat_cor_comp2[, i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1822
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1823 resultat = c()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1824
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1825 for(j in 1:length(col_mat_cor_comp1_i))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1826 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1827 cond = abs(col_mat_cor_comp1_i[j]) > cutoff_comp & abs(col_mat_cor_comp2_i[j]) > cutoff_comp
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1828
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1829 if(cond)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1830 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1831 resultat = c(resultat, j)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1832
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1833 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1834
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1835 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1836
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1837 return(resultat)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1838
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1839 }))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1840
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1841 indice_block_nomsBlock = sapply(1:length(nomsBlock), FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1842 res = which(colnames(mat_cor_comp1) == nomsBlock[i])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1843
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1844 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1845 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1846
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1847 boolean = FALSE
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1848 i = 1
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1849
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1850 while(i <=length(blockSelect) & !boolean)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1851 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1852 blockSelect_i = blockSelect[[i]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1853 cond = length(which(blockSelect_i%in%indice_block_nomsBlock == TRUE)) == length(nomsBlock)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1854
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1855 if(cond)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1856 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1857 boolean = TRUE
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1858
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1859 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1860
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1861 i = i + 1
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1862
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1863 } # Fin while(i <=length(blockSelect) & !boolean).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1864
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1865 varSelect = NULL
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1866
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1867 if(!boolean)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1868 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1869 cat(paste0("Erreur : les blocs : ", paste(nomsBlock, collapse = ", "), " ne peuvent pas être superposés.", "\n"))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1870
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1871 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1872 nomsBlockEtReponse = c(nomsBlock, "Y")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1873 indice1 = dataframe_Cor_Allcomp_Allvar$bloc%in%nomsBlockEtReponse
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1874 dataframe_Cor_Allcomp_Allvar2 = dataframe_Cor_Allcomp_Allvar[indice1, ]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1875 matCor_Allcomp_Allvar = apply(dataframe_Cor_Allcomp_Allvar2[, 3:4], 2, as.numeric)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1876 rownames(matCor_Allcomp_Allvar) = dataframe_Cor_Allcomp_Allvar2$variable
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1877
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1878 # indice permet de récupérer les variables de chaque bloc fortement corrélées avec soit
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1879 # la première composante ou la deuxième composante dans une partie du cercle de corrélation
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1880 # et de récupérer la variable réponse.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1881
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1882 indice = sapply(1:dim(dataframe_Cor_Allcomp_Allvar2)[1], FUN = function(k){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1883 cor1 = matCor_Allcomp_Allvar[k, 1]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1884 cor2 = matCor_Allcomp_Allvar[k, 2]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1885 blockEtReponse_k = dataframe_Cor_Allcomp_Allvar2[k, 2]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1886
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1887 if(blockEtReponse_k == "Y")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1888 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1889 cond2 = TRUE
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1890
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1891 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1892 cond1 = abs(cor1) > cutoff | abs(cor2) > cutoff
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1893
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1894 cond2 = cor1 > min.X & cor1 < max.X & cor2 > min.Y & cor2 < max.Y & cond1
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1895
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1896 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1897
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1898
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1899 return(cond2)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1900 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1901
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1902 dataframe_Cor_Allcomp_Allvar2[, 1:2] = apply(dataframe_Cor_Allcomp_Allvar2[, 1:2], 2, as.character)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1903 dataframe_Cor_Allcomp_Allvar2Select = dataframe_Cor_Allcomp_Allvar2[indice, ]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1904 varSelectTemp = dataframe_Cor_Allcomp_Allvar2Select$variable
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1905 ind_Y = which(dataframe_Cor_Allcomp_Allvar2Select$bloc == "Y")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1906 if(length(ind_Y) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1907 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1908 varSelect = varSelectTemp[- ind_Y]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1909
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1910 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1911 varSelect = varSelectTemp
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1912
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1913 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1914
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1915
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1916 matCor_Allcomp_AllvarSelect = matCor_Allcomp_Allvar[indice, , drop = FALSE]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1917
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1918
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1919
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1920 # Tracé de la superposition des cerles de corrélation.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1921 circle = list()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1922 circle[[1]] = ellipse(0, levels = 1, t = 1)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1923 circle[[2]] = ellipse(0, levels = 1, t = rad.in)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1924 circle = data.frame(do.call("rbind", circle), "Circle" = c(rep("Main circle", 100), rep("Inner circle", 100)))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1925
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1926 MainCircle = circle[grep("Main circle", circle[, 3]), ]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1927 InnerCircle = circle[grep("Inner circle", circle[, 3]), ]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1928
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1929 plot(MainCircle[, 1], MainCircle[, 2],
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1930 type = "l",
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1931 xlab = paste0("composante ", comp[1]),
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1932 ylab = paste0("composante ", comp[2]))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1933
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1934 points(InnerCircle[, 1], InnerCircle[, 2],
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1935 type = "l")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1936
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1937 if(dim(matCor_Allcomp_AllvarSelect)[1] != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1938 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1939
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1940 nom_blockEtReponseSelect = unique(dataframe_Cor_Allcomp_Allvar2Select$bloc)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1941 indice_blockEtReponseSelect = sapply(1:length(nom_blockEtReponseSelect), FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1942 ind = which(colnames(mat_cor_comp1) == nom_blockEtReponseSelect[i])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1943
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1944 if(length(ind) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1945 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1946 res = ind
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1947
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1948 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1949 res = dim(mat_cor_comp1)[1] + 1
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1950
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1951 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1952
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1953 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1954 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1955 vec_colSelect = vec_col[indice_blockEtReponseSelect]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1956
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1957 if(length(nom_blockEtReponseSelect) == 1)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1958 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1959 points(matCor_Allcomp_AllvarSelect[, 1], matCor_Allcomp_AllvarSelect[, 2],
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1960 col = NULL)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1961
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1962 text(matCor_Allcomp_AllvarSelect[, 1], matCor_Allcomp_AllvarSelect[, 2],
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1963 labels = rownames(matCor_Allcomp_AllvarSelect),
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1964 cex = cex,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1965 col = vec_colSelect[1])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1966
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1967 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1968
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1969 nbVarSelect_bloc = cumsum(sapply(1:length(nom_blockEtReponseSelect), FUN = function(j){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1970 res = length(which(dataframe_Cor_Allcomp_Allvar2Select$bloc == nom_blockEtReponseSelect[j]))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1971
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1972 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1973 }))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1974
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1975 for(i in 1:length(nbVarSelect_bloc))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1976 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1977 if(i == 1)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1978 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1979 indice1 = 1:nbVarSelect_bloc[1]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1980
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1981 if(length(indice1) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1982 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1983 matCor_Allcomp_AllvarSelect2 = matCor_Allcomp_AllvarSelect[indice1, , drop = FALSE]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1984
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1985 points(matCor_Allcomp_AllvarSelect2[, 1], matCor_Allcomp_AllvarSelect2[, 2],
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1986 col = NULL)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1987
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1988 text(matCor_Allcomp_AllvarSelect2[, 1], matCor_Allcomp_AllvarSelect2[, 2],
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1989 labels = rownames(matCor_Allcomp_AllvarSelect2),
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1990 cex = cex,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1991 col = rep(vec_colSelect[i], dim(matCor_Allcomp_AllvarSelect2)[1]))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1992
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1993 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1994 cat(paste0("Il n'y a de variables dans cette zone du cercle de corrélation pour le bloc ", nom_blockEtReponseSelect[i]), "\n")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1995
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1996
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1997 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1998
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
1999
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2000 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2001 indice2 = (nbVarSelect_bloc[i - 1] + 1):nbVarSelect_bloc[i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2002
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2003 if(length(indice2) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2004 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2005 matCor_Allcomp_AllvarSelect2 = matCor_Allcomp_AllvarSelect[indice2, , drop = FALSE]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2006
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2007 points(matCor_Allcomp_AllvarSelect2[, 1], matCor_Allcomp_AllvarSelect2[, 2],
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2008 col = NULL)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2009
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2010 text(matCor_Allcomp_AllvarSelect2[, 1], matCor_Allcomp_AllvarSelect2[, 2],
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2011 labels = rownames(matCor_Allcomp_AllvarSelect2),
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2012 cex = cex,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2013 col = rep(vec_colSelect[i], dim(matCor_Allcomp_AllvarSelect2)[1]))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2014
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2015
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2016 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2017 cat(paste0("Il n'y a de variables dans cette zone du cercle de corrélation pour le bloc ", nom_blockEtReponseSelect[i]), "\n")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2018
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2019 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2020
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2021
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2022 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2023
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2024 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2025
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2026 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2027
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2028 par(xpd = TRUE)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2029 legend(x = pos[1], y = pos[2],
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2030 legend = nom_blockEtReponseSelect,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2031 pch = pch,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2032 col = vec_colSelect,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2033 cex = cex_legend,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2034 inset = inset)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2035
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2036
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2037 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2038 cat("Il n'y a de variables dans cette zone du cercle de corrélation", "\n")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2039
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2040 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2041
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2042
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2043 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2044
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2045 return(varSelect)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2046
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2047
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2048 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2049
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2050 # La fonction networkVariable permet de tracer un réseau pour les variables de
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2051 # certains blocs et une variable réponse.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2052
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2053 networkVariable <-function(dataframe_Cor_Allcomp_Allvar,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2054 vec_Var,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2055 nomVar_block_Y,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2056 comp = 1:2,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2057 cutoff = 0
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2058 )
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2059 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2060 # Pour chaque variable de vec_Var et la variable réponse, nous récupérons les noms des blocs,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2061 # les corrélations entre la variable et chaque composante.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2062
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2063 ind = which(dataframe_Cor_Allcomp_Allvar$variable%in%vec_Var == TRUE)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2064 ind_Var_block_Y = which(dataframe_Cor_Allcomp_Allvar$variable == nomVar_block_Y)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2065
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2066 dataframe_Cor_Allcomp_AllvarSelect = dataframe_Cor_Allcomp_Allvar[c(ind, ind_Var_block_Y), ]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2067 nomBlocs = unique(dataframe_Cor_Allcomp_AllvarSelect$bloc)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2068
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2069 if((length(ind) == length(vec_Var)) & length(ind_Var_block_Y) == 1)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2070 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2071 if(length(nomBlocs) == 1)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2072 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2073 cat("Erreur : il n'y a des variables d'un seul bloc dans listeVar", "\n")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2074
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2075 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2076
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2077 liste_Cor_Allcomp_Allvar_bloc = lapply(1:length(nomBlocs), FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2078 nomBloc_i = nomBlocs[i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2079 indice = which(dataframe_Cor_Allcomp_AllvarSelect$bloc == nomBloc_i)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2080 resTemp = dataframe_Cor_Allcomp_AllvarSelect[indice, ]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2081
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2082 if(length(indice) == 1)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2083 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2084 res = resTemp
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2085
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2086 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2087 res = resTemp
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2088
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2089 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2090
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2091 rownames(res) = resTemp$variable
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2092
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2093 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2094 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2095 names(liste_Cor_Allcomp_Allvar_bloc) = nomBlocs
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2096
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2097 coord = lapply(1:length(liste_Cor_Allcomp_Allvar_bloc), FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2098 resTemp = liste_Cor_Allcomp_Allvar_bloc[[i]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2099 res = apply(resTemp[, comp + 2, drop = FALSE], 2, as.numeric)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2100
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2101 if(dim(resTemp)[1] == 1)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2102 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2103 res = matrix(res, nrow = 1)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2104
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2105 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2106
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2107 rownames(res) = resTemp$variable
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2108
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2109 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2110 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2111
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2112
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2113 l = 1
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2114 M_block = list()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2115 node.X1 = node.X2 = w = NULL
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2116
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2117 # Calcul de la similarité.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2118
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2119 for(j in 1:(length(nomBlocs) - 1))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2120 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2121 for(k in (j + 1):length(nomBlocs))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2122 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2123 M_block[[l]] = coord[[j]][, drop = FALSE] %*% t(coord[[k]][, drop = FALSE])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2124
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2125 X1 = rownames(coord[[j]])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2126 X2 = rownames(coord[[k]])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2127
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2128 rep.X1 = rep(X1, each = length(X2))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2129 rep.X2 = rep(X2, length(X1))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2130
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2131 node.X1= c(node.X1, rep.X1)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2132 node.X2 = c(node.X2, rep.X2)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2133
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2134 w = c(w, as.vector(t(M_block[[l]])))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2135
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2136 l = l + 1
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2137
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2138 } # Fin for(k in (j + 1):length(blocks)).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2139
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2140 } # Fin for(j in 1:(length(blocks) - 1)).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2141
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2142 # nodes
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2143 group = NULL
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2144 temp = lapply(1:length(liste_Cor_Allcomp_Allvar_bloc), function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2145 res = liste_Cor_Allcomp_Allvar_bloc[[i]]$variable
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2146
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2147 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2148 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2149 names(temp) = names(liste_Cor_Allcomp_Allvar_bloc)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2150
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2151 for (i in 1:length(temp))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2152 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2153 group = c(group, rep(names(temp)[i], length(temp[[i]])))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2154
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2155 } # Fin for (i in 1:length(temp)).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2156
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2157 nodes = data.frame(name = unlist(temp),
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2158 group = group)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2159
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2160 # gR
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2161 relations = data.frame(from = node.X1,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2162 to = node.X2,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2163 weight = w)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2164
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2165 idx = (abs(w) >= cutoff)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2166 relations = relations[idx, , drop = FALSE]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2167
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2168 gR = graph.data.frame(relations,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2169 directed = FALSE,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2170 vertices = nodes)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2171
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2172 gR = delete.vertices(gR, which(degree(gR) == 0))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2173
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2174 res = list(gR = gR)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2175
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2176 l = 1
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2177 for (i in 1:(length(nomBlocs)-1))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2178 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2179 for (j in (i + 1):length(nomBlocs))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2180 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2181 res[paste("M", names(liste_Cor_Allcomp_Allvar_bloc)[i], names(liste_Cor_Allcomp_Allvar_bloc)[j], sep="_")] = list(M_block[[l]])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2182 l = l + 1
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2183
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2184 } # Fin for (j in (i + 1):length(blocks)).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2185
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2186 } # Fin for (i in 1:(length(blocks)-1).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2187
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2188 res$cutoff = cutoff
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2189
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2190 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2191
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2192
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2193 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2194
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2195
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2196 # Fin if((length(which(ind))= length(listeVar)) & length(ind_Var_block_Y) == 1).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2197 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2198 if(length(ind) != length(vec_Var))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2199 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2200 cat("Erreur : les variables de vec_Var ne sont pas contenues dans dataframe_Cor_Allcomp_Allvar$variable.", "\n")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2201
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2202 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2203
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2204 if(length(ind_Var_block_Y) == 1)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2205 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2206 cat(paste0("Erreur : la variable réponse ", nomVar_block_Y," n'est pas contenue dans dataframe_Cor_Allcomp_Allvar$variable."), "\n")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2207
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2208
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2209 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2210
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2211 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2212
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2213
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2214 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2215
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2216
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2217
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2218 # Integration 7 blocs norm gene -------------------------------------------
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2219
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2220
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2221
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2222 # La fonction compute_cor_comp_var calcule, pour chaque variable d'un bloc, les corrélations
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2223 # entre la variable et les composantes sélectionnées par comp.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2224
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2225 compute_cor_comp_var <-function(res_block_splsda,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2226 comp = c(1:2))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2227 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2228 vec_blocksTemp = res_block_splsda$names$blocks
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2229 ind_Y = which(vec_blocksTemp == "Y")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2230 vec_blocks1 = vec_blocksTemp[- ind_Y]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2231 vec_indice_blocks = sapply(1:length(vec_blocks1), FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2232 res = which(res_block_splsda$names$blocks == vec_blocks1[i])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2233
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2234 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2235 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2236
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2237 # Calcul, pour chaque variable d'un bloc, des corrélations de cette variable avec
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2238 # les composantes dont les indices sont indiqués dans le vecteur comp.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2239
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2240 vec_blocks2 = c()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2241 liste_cor_comp_var_global = list()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2242
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2243 for(i in 1:length(vec_indice_blocks))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2244 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2245 indice_blocks_i = vec_indice_blocks[i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2246 block_i = res_block_splsda$names$blocks[indice_blocks_i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2247
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2248 vec_varSelect_i = c()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2249 liste_comp_i = list()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2250
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2251 for(j in 1:length(comp))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2252 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2253 indice_comp_j = comp[j]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2254 liste_comp_i[[j]] = res_block_splsda$variates[[indice_blocks_i]][, indice_comp_j]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2255 vec_varSelect_comp_j = selectVar(res_block_splsda,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2256 comp = indice_comp_j)[[indice_blocks_i]][[1]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2257
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2258 vec_varSelect_i = c(vec_varSelect_i, vec_varSelect_comp_j)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2259
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2260 } # Fin for(j in 1:length(comp)).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2261
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2262 vec_varSelect_i = unique(vec_varSelect_i)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2263
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2264 mat_block_i = res_block_splsda$X[[indice_blocks_i]][, vec_varSelect_i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2265
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2266 liste_cor_comp_var = list()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2267
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2268 for(j in 1:length(liste_comp_i))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2269 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2270 liste_cor_comp_var[[j]] = sapply(1:dim(mat_block_i)[2], FUN = function(k){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2271 cor(liste_comp_i[[j]], mat_block_i[, k])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2272 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2273
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2274 } # Fin for(j in 1:length(liste_comp_i)).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2275
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2276 mat_cor_Allcomp_Allvar = Reduce(cbind, liste_cor_comp_var)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2277 rownames(mat_cor_Allcomp_Allvar) = colnames(mat_block_i)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2278
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2279 vec_blocks_i = rep(block_i, dim(mat_block_i)[2])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2280 vec_blocks2 = c(vec_blocks2, vec_blocks_i)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2281
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2282 liste_cor_comp_var_global[[i]] = mat_cor_Allcomp_Allvar
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2283
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2284
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2285 } # Fin for(i in 1:length(blocks)).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2286
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2287
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2288 mat_cor_comp_var_global = Reduce(rbind, liste_cor_comp_var_global)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2289 dataframe_cor_comp_var_global = data.frame(cbind(rownames(mat_cor_comp_var_global),
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2290 vec_blocks2,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2291 mat_cor_comp_var_global))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2292
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2293 colnames(dataframe_cor_comp_var_global) = c("variable",
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2294 "bloc",
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2295 paste0("cor_var_comp", comp))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2296
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2297 dataframe_cor_comp_var_global[, 1:2] = apply(dataframe_cor_comp_var_global[, 1:2], 2, as.character)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2298 dataframe_cor_comp_var_global[, 3:dim(dataframe_cor_comp_var_global)[2]] = apply(dataframe_cor_comp_var_global[, 3:dim(dataframe_cor_comp_var_global)[2]], 2, as.numeric)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2299
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2300
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2301 return(dataframe_cor_comp_var_global)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2302
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2303 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2304
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2305 # La fonction composanteColin renvoie une liste. Le ième élément de cette liste
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2306 # contient les indices des blocs tels que, pour chaque paire de ces blocs, la
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2307 # première composante du bloc 1 est fortement corrélée à la première composante
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2308 # du bloc2 en valeur absolue et la deuxième composante du bloc 1 est fortement
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2309 # corrélée à la deuxième composante du bloc2 en valeur absolue.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2310
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2311 composanteColin <-function(mat_cor_comp1,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2312 mat_cor_comp2,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2313 cutoff_comp)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2314 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2315 res = list()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2316
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2317 index = 1:dim(mat_cor_comp1)[1]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2318 i = 1
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2319 compt = 1
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2320
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2321 while(length(index) != 0 & compt <= dim(mat_cor_comp1)[1])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2322 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2323 index_i = index[i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2324 res[[compt]] = c(index_i)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2325
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2326 index2 = index[-i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2327
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2328 if(length(index2) != 1)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2329 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2330
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2331 for(j in index2)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2332 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2333 if(length(res[[compt]]) == 1)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2334 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2335 if(abs(mat_cor_comp1[j, index_i]) > cutoff_comp & abs(mat_cor_comp2[j, index_i]) > cutoff_comp)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2336 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2337 res[[compt]] = c(res[[compt]], j)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2338 index = index[- c(which(index == j))]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2339
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2340 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2341
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2342 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2343
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2344 indice = sapply(1:length(res[[compt]]), FUN = function(k){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2345 index_k = res[[compt]][k]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2346 cond = abs(mat_cor_comp1[index_k, j]) > cutoff_comp & abs(mat_cor_comp2[index_k, j]) > cutoff_comp
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2347
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2348 return(cond)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2349 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2350
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2351 if(all(indice))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2352 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2353 res[[compt]] = c(res[[compt]], j)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2354 index = index[- c(which(index == j))]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2355
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2356 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2357
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2358
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2359 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2360
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2361 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2362
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2363 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2364 res[[compt]] = index_i
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2365
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2366 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2367
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2368 index = index[- c(which(index == index_i))]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2369 compt = compt + 1
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2370
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2371 } # Fin for(i in 1:dim(mat_cor_comp1)[2]).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2372
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2373 if(length(index) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2374 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2375 for(i in 1:length(index))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2376 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2377 res = c(res, list(index[i]))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2378
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2379 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2380
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2381 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2382
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2383
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2384 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2385 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2386
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2387
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2388 # La fonction compute_blockSelect permet de déterminer toutes les combinaisons
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2389 # possibles des blocs qui peuvent être superposés dans le cercle de corrélations
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2390 # et dont les variables peuvent être présentes dans le réseau.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2391
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2392 compute_blockSelect <-function(mat_cor_comp1,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2393 mat_cor_comp2,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2394 cutoff_comp)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2395 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2396
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2397 liste_vec_indice_blockSelect = composanteColin(mat_cor_comp1,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2398 mat_cor_comp2,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2399 cutoff_comp)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2400
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2401 vec_blocks = colnames(mat_cor_comp1)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2402 liste_vec_blocks = list()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2403
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2404 # liste_blocks est une liste contenant toutes les combinaisons possibles de blocs dont
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2405 # on peut superposer les cercles de corrélations et dont les variables peuvent être
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2406 # présentes dans le réseau.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2407
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2408 for(i in 1:length(liste_vec_indice_blockSelect))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2409 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2410 vec_indice_blockSelect_i = liste_vec_indice_blockSelect[[i]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2411
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2412 for(k in 1:length(vec_indice_blockSelect_i))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2413 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2414 matComb = combn(vec_indice_blockSelect_i, m = k)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2415
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2416 liste_vec_blocks_i = lapply(1:dim(matComb)[2], FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2417 comb_i = matComb[, i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2418 resultat = vec_blocks[comb_i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2419
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2420 return(resultat)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2421 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2422
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2423 for(j in 1:length(liste_vec_blocks_i))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2424 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2425 liste_vec_blocks = c(liste_vec_blocks, list(liste_vec_blocks_i[[j]]))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2426
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2427 } # Fin for(j in 1:length(liste_noms_blocks)).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2428
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2429
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2430 } # Fin for(k in 1:length(blockSelect_i)).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2431
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2432 } # Fin for(i in 1:length(blockSelect)).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2433
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2434 liste_vec_blocks = unique(liste_vec_blocks)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2435
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2436
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2437
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2438 return(list(liste_vec_indice_blockSelect = liste_vec_indice_blockSelect,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2439 liste_vec_blocks = liste_vec_blocks))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2440
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2441 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2442
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2443 # La fonction matCorEtBlockSelect permet de calculer la matrice de
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2444 # corrélation entre les comp[1] composantes de chaque bloc et la
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2445 # matrice de corrélation entre les comp[2] composantes de chaque
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2446 # bloc. Elle permet aussi de calculer, pour chaque variable d'un bloc,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2447 # les corrélations entre les composantes comp[1] et comp[2] et cette variable
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2448 # et de calculer toutes les combinaisons possibles des blocs pour lesquels nous
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2449 # pouvons superposer les cercles de corrélations.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2450
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2451 matCorEtBlockSelect <-function(res_block_splsda,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2452 cutoff_comp,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2453 comp)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2454 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2455 liste_mat_cor_comp = matriceCorrelation_comp(res_block_splsda = res_block_splsda,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2456 comp = comp)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2457
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2458 mat_cor_comp1 = liste_mat_cor_comp$mat_cor_comp1
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2459 mat_cor_comp2 = liste_mat_cor_comp$mat_cor_comp2
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2460
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2461
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2462 dataframe_cor_comp_var_global = compute_cor_comp_var(res_block_splsda = res_block_splsda,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2463 comp = comp)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2464
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2465
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2466 liste_blockSelect = compute_blockSelect(mat_cor_comp1 = mat_cor_comp1,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2467 mat_cor_comp2 = mat_cor_comp2,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2468 cutoff_comp = cutoff_comp)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2469
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2470 liste_vec_indice_blockSelect = liste_blockSelect$liste_vec_indice_blockSelect
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2471 liste_vec_blocks = liste_blockSelect$liste_vec_blocks
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2472
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2473 return(list(mat_cor_comp1 = mat_cor_comp1,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2474 mat_cor_comp2 = mat_cor_comp2,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2475 dataframe_cor_comp_var_global = dataframe_cor_comp_var_global,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2476 liste_vec_indice_blockSelect = liste_vec_indice_blockSelect,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2477 liste_vec_blocks = liste_vec_blocks))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2478
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2479 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2480
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2481 # La fonction addVariablesReponses permet de calculer, pour chaque
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2482 # variable réponse, la corrélation entre cette variable et la
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2483 # comp[1] composante et la corrélation entre cette variable et la comp[2]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2484 # composante pour chaque groupe de blocs.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2485
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2486 addVariablesReponses <-function(res_block_splsda,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2487 dataframe_cor_comp_var_global,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2488 liste_vec_indice_blockSelect,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2489 mat_block_Y)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2490 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2491 # On récupère les indices des composantes utilisées pour calculer les
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2492 # corrélations entre les variables des blocs et les composantes.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2493
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2494 comp = as.numeric(sapply(3:4, FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2495 col_i = colnames(dataframe_cor_comp_var_global)[i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2496 ch = strsplit(col_i, split = "_")[[1]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2497 resTemp = ch[length(ch)]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2498 res = substring(resTemp, nchar(resTemp), nchar(resTemp))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2499
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2500 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2501 }))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2502
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2503 # On calcule, pour chaque variable réponse, pour chaque composante du premier
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2504 # bloc du groupe de blocs, la corrélation entre cette variable réponse et la composante.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2505
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2506 liste_dataframe_cor_allcomp_varReponses = list()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2507 vec_groupe_blocks = c()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2508
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2509 for(i in 1:length(liste_vec_indice_blockSelect))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2510 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2511 vec_indice_blockSelect_i = liste_vec_indice_blockSelect[[i]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2512 indice_first_block_i = vec_indice_blockSelect_i[1]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2513
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2514 liste_comp_i = list()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2515 liste_cor_comp_var = list()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2516
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2517 for(j in 1:length(comp))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2518 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2519 indice_comp_j = comp[j]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2520 comp_j = res_block_splsda$variates[[indice_first_block_i]][, indice_comp_j]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2521
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2522 liste_cor_comp_var[[j]] = sapply(1:dim(mat_block_Y)[2], FUN = function(k){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2523 cor(comp_j, mat_block_Y[, k])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2524 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2525
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2526 } # Fin for(j in 1:length(liste_comp_i)).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2527
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2528 mat_cor_allcomp_varReponses = Reduce(cbind, liste_cor_comp_var)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2529 rownames(mat_cor_allcomp_varReponses) = colnames(mat_block_Y)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2530
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2531 dataframe_allcomp_varReponses = data.frame(colnames(mat_block_Y),
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2532 rep("Y", dim(mat_block_Y)[2]),
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2533 mat_cor_allcomp_varReponses)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2534
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2535 colnames(dataframe_allcomp_varReponses) = c("variable",
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2536 "bloc",
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2537 paste0("cor_var_comp", comp))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2538
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2539
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2540 liste_dataframe_cor_allcomp_varReponses[[i]] = dataframe_allcomp_varReponses
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2541
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2542 groupe_blocks_i = res_block_splsda$names$blocks[vec_indice_blockSelect_i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2543 vec_groupe_blocks = c(vec_groupe_blocks, paste(groupe_blocks_i, collapse = "-"))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2544
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2545
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2546 } # Fin for(in in 1:length(blockSelect)).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2547
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2548 names(liste_dataframe_cor_allcomp_varReponses) = vec_groupe_blocks
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2549
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2550 liste_dataframe_cor_comp_var_global = list()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2551
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2552 for(i in 1:length(liste_vec_indice_blockSelect))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2553 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2554 vec_indice_blockSelect_i = liste_vec_indice_blockSelect[[i]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2555 groupe_blocks_i = res_block_splsda$names$blocks[vec_indice_blockSelect_i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2556 indice_i = which(dataframe_cor_comp_var_global$bloc%in%groupe_blocks_i == TRUE)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2557 dataframe_cor_comp_var_global_indice_i = dataframe_cor_comp_var_global[indice_i, ]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2558
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2559 dataframe_cor_comp_varBlockEtVarRep_global = rbind(dataframe_cor_comp_var_global_indice_i,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2560 liste_dataframe_cor_allcomp_varReponses[[i]])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2561
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2562 dataframe_cor_comp_varBlockEtVarRep_global[, 1:2] = apply(dataframe_cor_comp_varBlockEtVarRep_global[, 1:2], 2, as.character)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2563 dataframe_cor_comp_varBlockEtVarRep_global[, 3:dim(dataframe_cor_comp_varBlockEtVarRep_global)[2]] = apply(dataframe_cor_comp_varBlockEtVarRep_global[, 3:dim(dataframe_cor_comp_varBlockEtVarRep_global)[2]], 2, as.numeric)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2564
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2565
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2566 liste_dataframe_cor_comp_var_global[[i]] = dataframe_cor_comp_varBlockEtVarRep_global
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2567
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2568
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2569 } # Fin for(i in 1:length(indice_blockSelect)).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2570
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2571 names(liste_dataframe_cor_comp_var_global) = vec_groupe_blocks
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2572
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2573
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2574 return(liste_dataframe_cor_comp_var_global)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2575
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2576 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2577
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2578 # La fonction addVariablesReponsesModified permet de calculer, pour chaque
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2579 # variable réponse, la corrélation entre cette variable et la
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2580 # comp[1] composante et la corrélation entre cette variable et la comp[2]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2581 # composante pour chaque groupe de blocs.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2582
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2583 addVariablesReponsesModified <-function(res_block_splsda,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2584 dataframe_cor_comp_var_global,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2585 liste_vec_indice_blockSelect,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2586 mat_block_Y)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2587 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2588 # On récupère les indices des composantes utilisées pour calculer les
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2589 # corrélations entre les variables des blocs et les composantes.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2590
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2591 comp = as.numeric(sapply(3:4, FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2592 col_i = colnames(dataframe_cor_comp_var_global)[i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2593 ch = strsplit(col_i, split = "_")[[1]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2594 resTemp = ch[length(ch)]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2595 res = substring(resTemp, nchar(resTemp), nchar(resTemp))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2596
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2597 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2598 }))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2599
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2600 # On calcule, pour chaque variable réponse, pour chaque composante du premier
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2601 # bloc du groupe de blocs, la corrélation entre cette variable réponse et la composante.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2602
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2603 liste_dataframe_cor_allcomp_varReponses = list()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2604 vec_groupe_blocks = c()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2605
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2606 for(i in 1:length(liste_vec_indice_blockSelect))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2607 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2608 vec_indice_blockSelect_i = liste_vec_indice_blockSelect[[i]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2609 indice_first_block_i = vec_indice_blockSelect_i[1]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2610
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2611 liste_comp_i = list()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2612 liste_cor_comp_var = list()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2613
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2614 for(j in 1:length(comp))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2615 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2616 indice_comp_j = comp[j]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2617 comp_j = res_block_splsda$variates[[indice_first_block_i]][, indice_comp_j]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2618
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2619 liste_cor_comp_var[[j]] = sapply(1:dim(mat_block_Y)[2], FUN = function(k){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2620 resTemp = comp_j%*%mat_block_Y[, k]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2621 res = resTemp/(norm(comp_j - mean(comp_j), "2")*norm(mat_block_Y[, k], "2"))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2622 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2623
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2624 } # Fin for(j in 1:length(liste_comp_i)).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2625
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2626 mat_cor_allcomp_varReponses = Reduce(cbind, liste_cor_comp_var)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2627 rownames(mat_cor_allcomp_varReponses) = colnames(mat_block_Y)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2628
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2629 dataframe_allcomp_varReponses = data.frame(colnames(mat_block_Y),
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2630 rep("Y", dim(mat_block_Y)[2]),
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2631 mat_cor_allcomp_varReponses)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2632
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2633 colnames(dataframe_allcomp_varReponses) = c("variable",
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2634 "bloc",
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2635 paste0("cor_var_comp", comp))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2636
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2637
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2638 liste_dataframe_cor_allcomp_varReponses[[i]] = dataframe_allcomp_varReponses
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2639
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2640 groupe_blocks_i = res_block_splsda$names$blocks[vec_indice_blockSelect_i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2641 vec_groupe_blocks = c(vec_groupe_blocks, paste(groupe_blocks_i, collapse = "-"))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2642
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2643
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2644 } # Fin for(in in 1:length(blockSelect)).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2645
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2646 names(liste_dataframe_cor_allcomp_varReponses) = vec_groupe_blocks
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2647
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2648 liste_dataframe_cor_comp_var_global = list()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2649
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2650 for(i in 1:length(liste_vec_indice_blockSelect))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2651 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2652 vec_indice_blockSelect_i = liste_vec_indice_blockSelect[[i]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2653 groupe_blocks_i = res_block_splsda$names$blocks[vec_indice_blockSelect_i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2654 indice_i = which(dataframe_cor_comp_var_global$bloc%in%groupe_blocks_i == TRUE)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2655 dataframe_cor_comp_var_global_indice_i = dataframe_cor_comp_var_global[indice_i, ]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2656
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2657 dataframe_cor_comp_varBlockEtVarRep_global = rbind(dataframe_cor_comp_var_global_indice_i,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2658 liste_dataframe_cor_allcomp_varReponses[[i]])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2659
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2660 dataframe_cor_comp_varBlockEtVarRep_global[, 1:2] = apply(dataframe_cor_comp_varBlockEtVarRep_global[, 1:2], 2, as.character)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2661 dataframe_cor_comp_varBlockEtVarRep_global[, 3:dim(dataframe_cor_comp_varBlockEtVarRep_global)[2]] = apply(dataframe_cor_comp_varBlockEtVarRep_global[, 3:dim(dataframe_cor_comp_varBlockEtVarRep_global)[2]], 2, as.numeric)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2662
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2663
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2664 liste_dataframe_cor_comp_var_global[[i]] = dataframe_cor_comp_varBlockEtVarRep_global
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2665
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2666
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2667 } # Fin for(i in 1:length(indice_blockSelect)).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2668
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2669 names(liste_dataframe_cor_comp_var_global) = vec_groupe_blocks
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2670
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2671
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2672 return(liste_dataframe_cor_comp_var_global)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2673
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2674 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2675
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2676
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2677 # La fonction circleCor permet de zoomer sur un rectangle du cercle de corrélations
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2678 # et de récupérer les variables des blocs dans cette partie zoomée du cercle de
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2679 # corrélations.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2680
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2681 circleCor <-function(liste_dataframe_cor_comp_var_global,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2682 liste_vec_indice_blockSelect,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2683 mat_cor_comp1,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2684 mat_cor_comp2,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2685 vec_blocks,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2686 nomsVarReponses,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2687 cutoff = 0.85,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2688 min.X = -1,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2689 max.X = 1,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2690 min.Y = -1,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2691 max.Y = 1,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2692 vec_col = colorRampPalette(brewer.pal(9, "Spectral"))(dim(mat_cor_comp1)[1] + 1),
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2693 rad.in = 0.5,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2694 cex = 0.7,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2695 cex_legend = 0.8,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2696 pos = c(1.2, 0),
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2697 pch = 20,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2698 inset = c(-0.25, 0))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2699 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2700
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2701 # On vérifie que nous pouvons superposer les cercles de corrélation.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2702
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2703 vec_indice_blocks = sapply(1:length(vec_blocks), FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2704 res = which(colnames(mat_cor_comp1) == vec_blocks[i])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2705
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2706 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2707 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2708
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2709 boolean = FALSE
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2710 i = 1
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2711
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2712 while(i <= length(liste_vec_indice_blockSelect) & !boolean)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2713 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2714 vec_indice_blockSelect_i = liste_vec_indice_blockSelect[[i]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2715 cond = length(which(vec_indice_blockSelect_i%in%vec_indice_blocks == TRUE)) == length(vec_blocks)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2716
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2717 if(cond)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2718 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2719 boolean = TRUE
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2720
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2721 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2722
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2723 i = i + 1
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2724
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2725 } # Fin while(i <= length(liste_vec_indice_blockSelect) & !boolean).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2726
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2727 varSelect = NULL
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2728
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2729 if(!boolean)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2730 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2731 stop(paste0("The blocks : ", paste(vec_blocks, collapse = ", "), " can not be superimposed."))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2732
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2733 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2734 # On récupère le groupe de blocs auxquels appartient vec_blocks.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2735
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2736 indice_nomsBlock = sapply(1:length(liste_dataframe_cor_comp_var_global), FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2737 name_iTemp = names(liste_dataframe_cor_comp_var_global)[i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2738 name_i = strsplit(name_iTemp, split = "-")[[1]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2739 res = all(vec_blocks%in%name_i)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2740
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2741 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2742 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2743
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2744 dataframe_cor_comp_var_global = liste_dataframe_cor_comp_var_global[[which(indice_nomsBlock == TRUE)]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2745 dataframe_cor_comp_var_globalTemp1 = dataframe_cor_comp_var_global
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2746
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2747 indice_nomsVarReponses = all(nomsVarReponses%in%dataframe_cor_comp_var_globalTemp1$variable)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2748
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2749 if(!indice_nomsVarReponses)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2750 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2751 stop("All the correlations between the response variables and the first component and the correlations
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2752 between the responses variables and the second component have not been computed.")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2753
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2754 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2755 comp = as.numeric(sapply(3:4, FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2756 col_i = colnames(dataframe_cor_comp_var_globalTemp1)[i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2757 ch = strsplit(col_i, split = "_")[[1]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2758 resTemp = ch[length(ch)]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2759 res = substring(resTemp, nchar(resTemp), nchar(resTemp))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2760
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2761 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2762 }))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2763
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2764
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2765 mat_cor_comp_var_globalTemp1 = t(sapply(1:dim(dataframe_cor_comp_var_globalTemp1)[1], FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2766 dataframe_cor_comp_var_globalTemp1_i = dataframe_cor_comp_var_globalTemp1[i, ]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2767 block_i = dataframe_cor_comp_var_globalTemp1_i$bloc
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2768 cor1 = dataframe_cor_comp_var_globalTemp1_i[paste0("cor_var_comp", comp[1])]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2769 cor2 = dataframe_cor_comp_var_globalTemp1_i[paste0("cor_var_comp", comp[2])]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2770
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2771 if(block_i == "Y")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2772 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2773 cor1_sign = cor1
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2774 cor2_sign = cor2
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2775
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2776 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2777 indice_block_comp1_i = which(colnames(mat_cor_comp1) == block_i)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2778 indice_block_comp2_i = which(colnames(mat_cor_comp2) == block_i)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2779
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2780 cor1_sign = sign(mat_cor_comp1[vec_indice_blocks[1], indice_block_comp1_i])*cor1
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2781 cor2_sign = sign(mat_cor_comp2[vec_indice_blocks[1], indice_block_comp2_i])*cor2
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2782
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2783 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2784
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2785 res = c(dataframe_cor_comp_var_globalTemp1_i[1:2], cor1_sign, cor2_sign)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2786
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2787 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2788 }))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2789
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2790 dataframe_cor_comp_var_globalTemp2 = as.data.frame(mat_cor_comp_var_globalTemp1)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2791 dataframe_cor_comp_var_globalTemp2[, 1:2] = apply(dataframe_cor_comp_var_globalTemp2[, 1:2], 2, as.character)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2792 colnames(dataframe_cor_comp_var_globalTemp2) = colnames(dataframe_cor_comp_var_global)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2793
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2794 # Pour les variables de vec_blocks et les variables réponses nomsVarReponses, on récupère les corrélations
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2795 # entre ces variables et les composantes.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2796
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2797 indice1 = sapply(1:dim(dataframe_cor_comp_var_globalTemp2)[1], FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2798 block_i = dataframe_cor_comp_var_globalTemp2$bloc[i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2799
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2800 if(block_i == "Y")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2801 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2802 res = dataframe_cor_comp_var_globalTemp2$variable[i]%in%nomsVarReponses
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2803
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2804 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2805 res = block_i%in%vec_blocks
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2806
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2807 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2808
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2809 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2810 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2811 dataframe_cor_comp_var_global2 = dataframe_cor_comp_var_globalTemp2[indice1, ]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2812 mat_cor_comp_var_global2 = apply(dataframe_cor_comp_var_global2[ , 3:4], 2, as.numeric)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2813 rownames(mat_cor_comp_var_global2) = dataframe_cor_comp_var_global2$variable
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2814
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2815 # indice permet de récupérer les variables de chaque bloc fortement corrélées avec soit
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2816 # la première composante ou la deuxième composante dans un rectangle du cercle de corrélations
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2817 # et de récupérer les variables réponses.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2818
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2819 indice2 = sapply(1:dim(dataframe_cor_comp_var_global2)[1], FUN = function(k){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2820 cor1 = mat_cor_comp_var_global2[k, 1]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2821 cor2 = mat_cor_comp_var_global2[k, 2]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2822 blockEtReponse_k = dataframe_cor_comp_var_global2[k, 2]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2823
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2824 if(blockEtReponse_k == "Y")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2825 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2826 cond2 = TRUE
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2827
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2828 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2829 cond1 = abs(cor1) > cutoff | abs(cor2) > cutoff
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2830
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2831 cond2 = cor1 > min.X & cor1 < max.X & cor2 > min.Y & cor2 < max.Y & cond1
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2832
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2833 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2834
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2835 return(cond2)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2836 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2837
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2838 dataframe_cor_comp_var_global2Select = dataframe_cor_comp_var_global2[indice2, ]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2839 varSelectTemp = dataframe_cor_comp_var_global2Select$variable
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2840 ind_Y = which(dataframe_cor_comp_var_global2Select$bloc == "Y")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2841
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2842 if(length(ind_Y) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2843 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2844 varSelect = varSelectTemp[- ind_Y]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2845
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2846 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2847 varSelect = varSelectTemp
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2848
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2849 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2850
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2851 mat_cor_comp_var_global2Select = mat_cor_comp_var_global2[indice2, , drop = FALSE]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2852
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2853
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2854 # Tracé de la superposition des cerles de corrélation.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2855 circle = list()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2856 circle[[1]] = ellipse(0, levels = 1, t = 1)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2857 circle[[2]] = ellipse(0, levels = 1, t = rad.in)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2858 circle = data.frame(do.call("rbind", circle), "Circle" = c(rep("Main circle", 100), rep("Inner circle", 100)))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2859
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2860 MainCircle = circle[grep("Main circle", circle[, 3]), ]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2861 InnerCircle = circle[grep("Inner circle", circle[, 3]), ]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2862
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2863 plot(MainCircle[, 1], MainCircle[, 2],
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2864 type = "l",
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2865 xlab = paste0("composante ", comp[1]),
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2866 ylab = paste0("composante ", comp[2]))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2867
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2868 points(InnerCircle[, 1], InnerCircle[, 2],
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2869 type = "l")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2870
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2871 if(dim(mat_cor_comp_var_global2Select)[1] != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2872 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2873 vec_blockEtReponseSelect = unique(dataframe_cor_comp_var_global2Select$bloc)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2874 indice_blockEtReponseSelect = sapply(1:length(vec_blockEtReponseSelect), FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2875 ind = which(colnames(mat_cor_comp1) == vec_blockEtReponseSelect[i])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2876
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2877 if(length(ind) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2878 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2879 res = ind
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2880
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2881 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2882 res = dim(mat_cor_comp1)[1] + 1
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2883
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2884 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2885
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2886 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2887 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2888 vec_colSelect = vec_col[indice_blockEtReponseSelect]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2889
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2890 if(length(vec_blockEtReponseSelect) == 1)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2891 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2892 points(mat_cor_comp_var_global2Select[, 1], mat_cor_comp_var_global2Select[, 2],
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2893 col = NULL)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2894
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2895 text(mat_cor_comp_var_global2Select[, 1], mat_cor_comp_var_global2Select[, 2],
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2896 labels = rownames(mat_cor_comp_var_global2Select),
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2897 cex = cex,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2898 col = vec_colSelect[1])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2899
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2900 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2901
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2902 nbVarSelect_bloc = cumsum(sapply(1:length(vec_blockEtReponseSelect), FUN = function(j){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2903 res = length(which(dataframe_cor_comp_var_global2Select$bloc == vec_blockEtReponseSelect[j]))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2904
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2905 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2906 }))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2907
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2908 for(i in 1:length(nbVarSelect_bloc))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2909 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2910 if(i == 1)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2911 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2912 indice_nbVar1 = 1:nbVarSelect_bloc[1]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2913
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2914 mat_cor_comp_var_global2Select2 = mat_cor_comp_var_global2Select[indice_nbVar1, , drop = FALSE]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2915
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2916 points(mat_cor_comp_var_global2Select2[, 1], mat_cor_comp_var_global2Select2[, 2],
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2917 col = NULL)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2918
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2919 text(mat_cor_comp_var_global2Select2[, 1], mat_cor_comp_var_global2Select2[, 2],
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2920 labels = rownames(mat_cor_comp_var_global2Select2),
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2921 cex = cex,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2922 col = rep(vec_colSelect[i], dim(mat_cor_comp_var_global2Select2)[1]))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2923
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2924
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2925 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2926 indice_nbVar2 = (nbVarSelect_bloc[i - 1] + 1):nbVarSelect_bloc[i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2927
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2928
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2929 mat_cor_comp_var_global2Select2 = mat_cor_comp_var_global2Select[indice_nbVar2, , drop = FALSE]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2930
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2931 points(mat_cor_comp_var_global2Select2[, 1], mat_cor_comp_var_global2Select2[, 2],
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2932 col = NULL)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2933
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2934 text(mat_cor_comp_var_global2Select2[, 1], mat_cor_comp_var_global2Select2[, 2],
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2935 labels = rownames(mat_cor_comp_var_global2Select2),
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2936 cex = cex,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2937 col = rep(vec_colSelect[i], dim(mat_cor_comp_var_global2Select2)[1]))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2938
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2939
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2940 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2941
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2942 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2943
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2944 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2945
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2946 par(xpd = TRUE)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2947 legend(x = pos[1], y = pos[2],
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2948 legend = vec_blockEtReponseSelect,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2949 pch = pch,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2950 col = vec_colSelect,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2951 cex = cex_legend,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2952 inset = inset)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2953
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2954
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2955 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2956 warning("There is no variables in this rectangle of the correlation circle.")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2957
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2958 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2959
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2960
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2961 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2962
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2963
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2964
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2965 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2966
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2967 return(varSelect)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2968
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2969
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2970 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2971
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2972 tabVarSelect <-function(varSelect)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2973 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2974
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2975
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2976 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2977
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2978 # La fonction compute_matSimilarity calcule, pour chaque groupe de blocs, les
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2979 # similarités entre le bloc1 et le bloc2 et entre les blocs et la réponse.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2980
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2981 compute_matSimilarity <-function(liste_dataframe_cor_comp_var_global)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2982 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2983 comp = as.numeric(sapply(3:4, FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2984 col_i = colnames(liste_dataframe_cor_comp_var_global[[1]])[i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2985 ch = strsplit(col_i, split = "_")[[1]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2986 resTemp = ch[length(ch)]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2987 res = substring(resTemp, nchar(resTemp), nchar(resTemp))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2988
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2989 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2990 }))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2991
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2992 liste_matSimilarity_group = list()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2993
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2994 # On calcule, pour chaque groupe de blocs, les matrices de similarités entre
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2995 # chaque paire de blocs.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2996
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2997 for(i in 1:length(liste_dataframe_cor_comp_var_global))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2998 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
2999 dataframe_cor_comp_var_global_i = liste_dataframe_cor_comp_var_global[[i]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3000 blocks_i = unique(dataframe_cor_comp_var_global_i$bloc)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3001
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3002 coord = lapply(1:length(blocks_i), FUN = function(j){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3003 ind_j = which(dataframe_cor_comp_var_global_i$bloc == blocks_i[j])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3004 dataframe_cor_comp_var_global_i_j = dataframe_cor_comp_var_global_i[ind_j, paste0("cor_var_comp", comp)]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3005 res = as.matrix(dataframe_cor_comp_var_global_i_j, drop = FALSE)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3006 rownames(res) = rownames(dataframe_cor_comp_var_global_i_j)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3007
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3008 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3009 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3010
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3011 M_block = list()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3012 l = 1
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3013
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3014 vec_blocks_i = c()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3015
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3016 for(j in 1:(length(blocks_i) - 1))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3017 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3018 blocks_i_j = blocks_i[j]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3019
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3020 for(k in (j + 1):length(blocks_i))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3021 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3022 blocks_i_k = blocks_i[k]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3023
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3024 M_block[[l]] = coord[[j]][, drop = FALSE] %*% t(coord[[k]][, drop = FALSE])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3025 rownames(M_block[[l]]) = rownames(coord[[j]])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3026 colnames(M_block[[l]]) = rownames(coord[[k]])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3027
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3028 blocks_j_k = paste(c(blocks_i_j, blocks_i_k), collapse = "-")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3029 vec_blocks_i = c(vec_blocks_i, blocks_j_k)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3030
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3031 l = l + 1
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3032
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3033 } # Fin for(k in (j + 1):length(blocks)).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3034
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3035 } # Fin for(j in 1:(length(blocks) - 1)).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3036 names(M_block) = vec_blocks_i
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3037
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3038 liste_matSimilarity_group[[i]] = M_block
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3039
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3040 } # Fin for(i in 1:length(liste_dataframe_Cor_comp_var_global)).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3041
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3042 names(liste_matSimilarity_group) = names(liste_dataframe_cor_comp_var_global)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3043
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3044 return(list(liste_matSimilarity_group = liste_matSimilarity_group,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3045 comp = comp))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3046
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3047 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3048
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3049 # La fonction networkVariableSelect permet de tracer un réseau pour les variables de
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3050 # certains blocs et des variables réponses.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3051
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3052 networkVariableSelect <-function(liste_matSimilarity_group,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3053 comp,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3054 res_block_splsda,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3055 cutoff_comp = 0.8,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3056 vec_varBlock,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3057 vec_varRep,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3058 cutoff = 0
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3059 )
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3060 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3061
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3062 vec_varBlockEtReponse = c(vec_varBlock, vec_varRep)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3063
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3064 # Nous vérifions que nous pouvons créer un réseau pour les variables des
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3065 # blocs vec_Var_blockEtReponse.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3066
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3067 # Nous recherchons le groupe de blocs associé à vec_varBlock.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3068
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3069 indice_group_vecVar = sapply(1:length(liste_matSimilarity_group), FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3070 liste_matSimilarity_group_i = liste_matSimilarity_group[[i]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3071 boolean = FALSE
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3072 j = 1
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3073
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3074 while((j <= length(liste_matSimilarity_group_i))&!boolean)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3075 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3076 matSimilarity_group_i_j = liste_matSimilarity_group_i[[j]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3077 vec_var_block1 = rownames(matSimilarity_group_i_j)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3078 vec_var_block2 = colnames(matSimilarity_group_i_j)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3079
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3080 vec_var_block = c(vec_var_block1, vec_var_block2)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3081
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3082 if(any(vec_var_block%in%vec_varBlock))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3083 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3084 boolean = TRUE
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3085
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3086 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3087
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3088 j = j + 1
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3089
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3090 } # Fin while((j <= length(liste_matSimilarity_group_i))&!boolean).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3091
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3092 res = boolean
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3093
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3094 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3095 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3096
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3097 res = NULL
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3098
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3099 if(length(which(indice_group_vecVar == TRUE)) >= 2)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3100 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3101 cat("Erreur : les variables de vec_varBlock. doivent appartenir à un seul élément de la liste
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3102 liste_res_matSimilarity_group$liste_matSimilarity_group.", "\n")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3103
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3104 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3105 liste_matSimilarity = liste_matSimilarity_group[[which(indice_group_vecVar == TRUE)]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3106
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3107 blocks_liste_matSimilarityTemp1 = sapply(1:length(liste_matSimilarity), FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3108 noms_block1_block2_i = names(liste_matSimilarity)[i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3109 ch = strsplit(noms_block1_block2_i, split = "-")[[1]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3110 block1 = ch[1]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3111 block2 = ch[2]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3112 res = c(block1, block2)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3113
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3114 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3115 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3116
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3117 blocks_liste_matSimilarity = unique(as.vector(blocks_liste_matSimilarityTemp1))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3118
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3119 indice_blocks_liste_matSimilarityTemp = sapply(1:length(blocks_liste_matSimilarity), FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3120 res = which(res_block_splsda$names$blocks == blocks_liste_matSimilarity[i])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3121
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3122 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3123 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3124
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3125 ind_Y = which(res_block_splsda$names$blocks == "Y")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3126 indice_blocks_liste_matSimilarity = indice_blocks_liste_matSimilarityTemp[indice_blocks_liste_matSimilarityTemp != ind_Y]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3127
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3128 boolean_pos_cor = TRUE
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3129
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3130 # Nous vérifions que les ièmes composantes de chaque bloc sont fortement corrélées positivement.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3131
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3132 if(length(indice_blocks_liste_matSimilarity) == 1)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3133 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3134
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3135
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3136 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3137 for(i in 1:length(comp))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3138 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3139 comp_i = comp[i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3140
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3141 for(j in 1:(length(indice_blocks_liste_matSimilarity) - 1))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3142 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3143 indice_blocks_liste_matSimilarity_j = indice_blocks_liste_matSimilarity[j]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3144 comp_indice_blocks_liste_matSimilarity_j = res_block_splsda$variates[[indice_blocks_liste_matSimilarity_j]][, comp_i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3145
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3146
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3147 for(k in (j + 1):length(indice_blocks_liste_matSimilarity))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3148 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3149 indice_blocks_liste_matSimilarity_k = indice_blocks_liste_matSimilarity[k]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3150 comp_indice_blocks_liste_matSimilarity_k = res_block_splsda$variates[[indice_blocks_liste_matSimilarity_k]][, comp_i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3151
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3152 cor = cor(comp_indice_blocks_liste_matSimilarity_j, comp_indice_blocks_liste_matSimilarity_k)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3153
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3154 boolean_pos_cor = boolean_pos_cor & all(cor > cutoff_comp)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3155
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3156
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3157 } # Fin for(k in (j + 1):length(indice_blocks_liste_matSimilarity)).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3158
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3159 } # Fin for(j in 1:(length(indice_blocks_liste_matSimilarity) - 1)).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3160
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3161 } # Fin for(i in 1:length(comp)).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3162
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3163
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3164 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3165
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3166
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3167
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3168 if(!boolean_pos_cor)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3169 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3170 cat("Erreur : pour chaque paire de bloc, la ième composante de chaque bloc doivent être corrélées positivement afin de pouvoir créer
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3171 un réseau.", "\n")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3172
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3173 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3174 # Nous récupérons les matrices de similarités associés aux variables de vec_varBlockEtReponse .
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3175
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3176 liste_matSimilaritySelectTemp = lapply(1:length(liste_matSimilarity), FUN = function(j){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3177 matSimilarity_j = liste_matSimilarity[[j]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3178
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3179 indice_row_matSimilarity_j = which(rownames(matSimilarity_j)%in%vec_varBlockEtReponse == TRUE)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3180 indice_col_matSimilarity_j = which(colnames(matSimilarity_j)%in%vec_varBlockEtReponse == TRUE)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3181
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3182 if((length(indice_row_matSimilarity_j) != 0) &(length(indice_col_matSimilarity_j) != 0))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3183 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3184 res = matSimilarity_j[indice_row_matSimilarity_j, indice_col_matSimilarity_j, drop = FALSE]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3185
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3186 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3187 res = NA
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3188
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3189 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3190
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3191 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3192 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3193 names(liste_matSimilaritySelectTemp) = names(liste_matSimilarity)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3194
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3195 indice_NA_liste_matSimilaritySelectTemp = sapply(1:length(liste_matSimilaritySelectTemp), FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3196 liste_matSimilaritySelectTemp_i = liste_matSimilaritySelectTemp[[i]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3197
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3198 if(is.matrix(liste_matSimilaritySelectTemp_i))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3199 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3200 res = FALSE
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3201
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3202 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3203 if(is.na(liste_matSimilaritySelectTemp_i))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3204 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3205 res = TRUE
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3206
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3207 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3208 res = FALSE
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3209
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3210 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3211
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3212 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3213
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3214 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3215 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3216
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3217
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3218
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3219 liste_matSimilaritySelect = liste_matSimilaritySelectTemp[!indice_NA_liste_matSimilaritySelectTemp]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3220
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3221 # Nous créons le réseau.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3222
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3223 w = c()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3224 node.X1 = c()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3225 node.X2 = c()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3226 vec_group = c()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3227 vec_nomsVar = c()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3228
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3229 for(i in 1:length(liste_matSimilaritySelect))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3230 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3231
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3232 noms_bloc1_bloc2 = names(liste_matSimilaritySelect)[i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3233 matSimilaritySelect_i = liste_matSimilaritySelect[[i]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3234
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3235 X1 = rownames(matSimilaritySelect_i)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3236 X2 = colnames(matSimilaritySelect_i)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3237
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3238 rep.X1 = rep(X1, each = length(X2))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3239 rep.X2 = rep(X2, length(X1))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3240
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3241 node.X1= c(node.X1, rep.X1)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3242 node.X2 = c(node.X2, rep.X2)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3243
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3244 ch = strsplit(noms_bloc1_bloc2, split = "-")[[1]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3245 nom_bloc1 = ch[1]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3246 nom_bloc2 = ch[2]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3247 vec_group = c(vec_group, c(rep(nom_bloc1, length(X1)), rep(nom_bloc2, length(X2))))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3248 vec_nomsVar = c(vec_nomsVar, c(X1, X2))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3249
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3250 w = c(w, as.vector(t(matSimilaritySelect_i)))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3251
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3252 } # Fin for(i in 1:length(liste_matSimilaritySelect)).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3253
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3254 dup = duplicated(vec_nomsVar)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3255 vec_nomsVar = vec_nomsVar[!dup]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3256 vec_group = vec_group[!dup]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3257
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3258 nodes = data.frame(name = vec_nomsVar,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3259 group = vec_group)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3260
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3261 # gR
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3262 relations = data.frame(from = node.X1,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3263 to = node.X2,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3264 weight = w)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3265
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3266 idx = (abs(w) >= cutoff)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3267 relations = relations[idx, , drop = FALSE]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3268
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3269 gR = graph.data.frame(relations,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3270 directed = FALSE,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3271 vertices = nodes)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3272
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3273 # On supprime les noeuds qui n'ont pas d'arêtes.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3274 gR = delete.vertices(gR, which(degree(gR) == 0))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3275
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3276 res = list(gR = gR)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3277 res$cutoff = cutoff
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3278
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3279
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3280
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3281 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3282
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3283
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3284 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3285
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3286 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3287
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3288 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3289
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3290 # La fonction networkVar permet de tracer un réseau pour certaines variables des
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3291 # blocs et des variables réponses.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3292
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3293 networkVar <-function(liste_matSimilarity_group = liste_matSimilarity_group,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3294 comp = comp,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3295 res_block_splsda,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3296 cutoff_comp = 0.8,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3297 vec_varBlock,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3298 vec_varRep,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3299 vec_varBlockInteret = NULL,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3300 cutoff = 0
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3301 )
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3302 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3303 # Nous vérifions que nous pouvons créer un réseau pour les variables des
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3304 # blocs vec_VarBlock.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3305
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3306 # Nous recherchons le groupe de blocs associé à vec_Var.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3307
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3308 indice_group_vecVar = sapply(1:length(liste_matSimilarity_group), FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3309 liste_matSimilarity_group_i = liste_matSimilarity_group[[i]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3310 boolean = FALSE
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3311 j = 1
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3312
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3313 while((j <= length(liste_matSimilarity_group_i))&!boolean)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3314 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3315 matSimilarity_group_i_j = liste_matSimilarity_group_i[[j]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3316 vec_var_block1 = rownames(matSimilarity_group_i_j)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3317 vec_var_block2 = colnames(matSimilarity_group_i_j)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3318
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3319 vec_var_block1_block2 = c(vec_var_block1, vec_var_block2)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3320
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3321 if(any(vec_var_block1_block2%in%vec_varBlock))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3322 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3323 boolean = TRUE
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3324
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3325 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3326
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3327 j = j + 1
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3328
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3329 } # Fin while((j <= length(liste_matSimilarity_group_i))&!boolean).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3330
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3331 res = boolean
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3332
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3333 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3334 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3335
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3336
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3337 if(length(which(indice_group_vecVar == TRUE)) >= 2)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3338 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3339 stop("The variables of vec_var have to belong to only one element of
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3340 liste_res_matSimilarity_group$liste_matSimilarity_group.")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3341
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3342 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3343 liste_matSimilarity = liste_matSimilarity_group[[which(indice_group_vecVar == TRUE)]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3344
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3345 if(!is.null(vec_varBlockInteret))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3346 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3347 AllVariables_vec = sapply(1:length(liste_matSimilarity), FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3348 matSimilarity_i = liste_matSimilarity[[i]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3349 res = c(rownames(matSimilarity_i), colnames(matSimilarity_i))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3350
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3351 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3352 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3353 AllVariables_vec = unique(unlist(AllVariables_vec))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3354
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3355 index_variableInterestNotInAllVariables_vec = vec_varBlockInteret%in%AllVariables_vec
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3356
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3357 if(length(which(index_variableInterestNotInAllVariables_vec == FALSE)) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3358 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3359 InterestVariableNotIn = vec_varBlockInteret[which(index_variableInterestNotInAllVariables_vec == FALSE)]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3360
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3361 warning(paste0("The variables of interest ", paste(InterestVariableNotIn, collapse = ","), " do not belong
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3362 to the variables of the blocks for which the network can be created. These variables will
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3363 be not in the network."))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3364 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3365
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3366 vec_varBlockInteret2 = vec_varBlockInteret[which(index_variableInterestNotInAllVariables_vec == TRUE)]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3367
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3368
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3369 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3370 vec_varBlockInteret2 = vec_varBlockInteret
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3371
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3372 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3373
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3374
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3375 if(!is.null(vec_varBlock) & !is.null(vec_varBlockInteret2))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3376 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3377 varCom = intersect(vec_varBlock, vec_varBlockInteret2)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3378
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3379 if(length(varCom) != 0)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3380 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3381 index_varCom = sapply(1:length(varCom), FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3382 res = which(vec_varBlock == varCom[i])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3383
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3384 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3385 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3386 vec_varBlock2 = vec_varBlock[- index_varCom]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3387
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3388 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3389 vec_varBlock2 = vec_varBlock
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3390
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3391 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3392
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3393 vec_varBlock3 = c(vec_varBlock2, vec_varBlockInteret2)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3394
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3395 }else if(!is.null(vec_varBlock) & is.null(vec_varBlockInteret2))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3396 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3397 vec_varBlock3 = vec_varBlock
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3398
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3399 }else if(is.null(vec_varBlock) & !is.null(vec_varBlockInteret2))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3400 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3401 vec_varBlock3 = vec_varBlockInteret2
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3402
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3403 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3404
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3405 vec_var = c(vec_varBlock3, vec_varRep)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3406
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3407
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3408
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3409 blocks_liste_matSimilarityTemp1 = sapply(1:length(liste_matSimilarity), FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3410 noms_block1_block2_i = names(liste_matSimilarity)[i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3411 ch = strsplit(noms_block1_block2_i, split = "-")[[1]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3412 block1 = ch[1]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3413 block2 = ch[2]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3414 res = c(block1, block2)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3415
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3416 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3417 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3418
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3419 blocks_liste_matSimilarity = unique(as.vector(blocks_liste_matSimilarityTemp1))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3420
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3421 indice_blocks_liste_matSimilarityTemp = sapply(1:length(blocks_liste_matSimilarity), FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3422 res = which(res_block_splsda$names$blocks == blocks_liste_matSimilarity[i])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3423
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3424 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3425 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3426
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3427 ind_Y = which(res_block_splsda$names$blocks == "Y")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3428 indice_blocks_liste_matSimilarity = indice_blocks_liste_matSimilarityTemp[indice_blocks_liste_matSimilarityTemp != ind_Y]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3429
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3430 boolean_pos_cor = TRUE
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3431
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3432 if(length(indice_blocks_liste_matSimilarity) == 1)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3433 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3434
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3435
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3436 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3437 for(i in 1:length(comp))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3438 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3439 comp_i = comp[i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3440
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3441 for(j in 1:(length(indice_blocks_liste_matSimilarity) - 1))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3442 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3443 indice_blocks_liste_matSimilarity_j = indice_blocks_liste_matSimilarity[j]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3444 comp_indice_blocks_liste_matSimilarity_j = res_block_splsda$variates[[indice_blocks_liste_matSimilarity_j]][, comp_i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3445
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3446
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3447 for(k in (j + 1):length(indice_blocks_liste_matSimilarity))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3448 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3449 indice_blocks_liste_matSimilarity_k = indice_blocks_liste_matSimilarity[k]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3450 comp_indice_blocks_liste_matSimilarity_k = res_block_splsda$variates[[indice_blocks_liste_matSimilarity_k]][, comp_i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3451
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3452 cor = cor(comp_indice_blocks_liste_matSimilarity_j, comp_indice_blocks_liste_matSimilarity_k)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3453
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3454 boolean_pos_cor = boolean_pos_cor & cor > cutoff_comp
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3455
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3456
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3457 } # Fin for(k in (j + 1):length(indice_blocks_vec_VarBlock)).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3458
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3459 } # Fin for(j in 1:(length(indice_blocks_vec_VarBlock)) - 1).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3460
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3461 } # Fin for(i in 1:length(comp)).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3462
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3463
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3464 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3465
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3466
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3467
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3468 if(!boolean_pos_cor)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3469 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3470 stop("For each pair of blocks, the ith component of the first block
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3471 and the ith component of the second block have to be positively correlated in order
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3472 to create a network.")
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3473
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3474 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3475 liste_matSimilaritySelectTemp = lapply(1:length(liste_matSimilarity), FUN = function(j){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3476 matSimilarity_j = liste_matSimilarity[[j]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3477
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3478 indice_row_matSimilarity_j = which(rownames(matSimilarity_j)%in%vec_var == TRUE)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3479 indice_col_matSimilarity_j = which(colnames(matSimilarity_j)%in%vec_var == TRUE)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3480
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3481 if((length(indice_row_matSimilarity_j) != 0) &(length(indice_col_matSimilarity_j) != 0))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3482 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3483 res = matSimilarity_j[indice_row_matSimilarity_j, indice_col_matSimilarity_j, drop = FALSE]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3484
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3485 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3486 res = NA
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3487
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3488 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3489
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3490 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3491 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3492 names(liste_matSimilaritySelectTemp) = names(liste_matSimilarity)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3493
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3494 indice_NA_liste_matSimilaritySelectTemp = sapply(1:length(liste_matSimilaritySelectTemp), FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3495 liste_matSimilaritySelectTemp_i = liste_matSimilaritySelectTemp[[i]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3496
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3497 if(is.matrix(liste_matSimilaritySelectTemp_i))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3498 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3499 res = FALSE
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3500
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3501 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3502 if(is.na(liste_matSimilaritySelectTemp_i))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3503 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3504 res = TRUE
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3505
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3506 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3507 res = FALSE
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3508
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3509 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3510
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3511 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3512
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3513 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3514 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3515
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3516
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3517 liste_matSimilaritySelect = liste_matSimilaritySelectTemp[!indice_NA_liste_matSimilaritySelectTemp]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3518
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3519 w = c()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3520 node.X1 = c()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3521 node.X2 = c()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3522 vec_group = c()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3523 vec_nomsVar = c()
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3524
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3525 for(i in 1:length(liste_matSimilaritySelect))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3526 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3527
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3528 noms_block1_block2 = names(liste_matSimilaritySelect)[i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3529 matSimilaritySelect_i = liste_matSimilaritySelect[[i]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3530
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3531 X1 = rownames(matSimilaritySelect_i)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3532 X2 = colnames(matSimilaritySelect_i)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3533
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3534 rep.X1 = rep(X1, each = length(X2))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3535 rep.X2 = rep(X2, length(X1))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3536
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3537 node.X1 = c(node.X1, rep.X1)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3538 node.X2 = c(node.X2, rep.X2)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3539
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3540 ch = strsplit(noms_block1_block2, split = "-")[[1]]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3541 nom_block1 = ch[1]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3542 nom_block2 = ch[2]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3543 vec_group = c(vec_group, c(rep(nom_block1, length(X1)), rep(nom_block2, length(X2))))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3544 vec_nomsVar = c(vec_nomsVar, c(X1, X2))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3545
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3546 w = c(w, as.vector(t(matSimilaritySelect_i)))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3547
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3548 } # Fin for(i in 1:length(liste_matSimilaritySelect)).
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3549
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3550 dup = duplicated(vec_nomsVar)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3551 vec_nomsVar = vec_nomsVar[!dup]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3552 vec_group = vec_group[!dup]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3553
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3554 nodes = data.frame(name = vec_nomsVar,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3555 group = vec_group)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3556
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3557 # gR
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3558 relations = data.frame(from = node.X1,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3559 to = node.X2,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3560 weight = w)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3561
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3562 # idx
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3563 if(!is.null(vec_varBlock) & !is.null(vec_varBlockInteret2) & !is.null(vec_varRep))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3564 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3565
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3566 idx = sapply(1:dim(relations)[1], FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3567 node.X1_i = relations$from[i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3568 node.X2_i = relations$to[i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3569
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3570 if(node.X1_i%in%vec_varBlockInteret2 | node.X2_i%in%vec_varBlockInteret2)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3571 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3572 res = TRUE
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3573
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3574 }else if(node.X1_i%in%vec_varRep | node.X2_i%in%vec_varRep){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3575 res = TRUE
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3576
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3577 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3578 res = abs(w)[i] >= cutoff
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3579
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3580 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3581
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3582 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3583 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3584
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3585 }else if(!is.null(vec_varBlock) & is.null(vec_varBlockInteret2) & !is.null(vec_varRep))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3586 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3587 idx = sapply(1:dim(relations)[1], FUN = function(i){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3588 node.X1_i = relations$from[i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3589 node.X2_i = relations$to[i]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3590
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3591 if(node.X1_i%in%vec_varRep | node.X2_i%in%vec_varRep){
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3592 res = TRUE
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3593
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3594 }else{
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3595 res = abs(w)[i] >= cutoff
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3596
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3597 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3598
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3599 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3600 })
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3601
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3602 }else if(is.null(vec_varBlockEtReponse) & !is.null(vec_varBlockInteret2) & !is.null(vec_varRep))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3603 {
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3604 idx = rep(TRUE, dim(relations)[1])
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3605
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3606 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3607
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3608 relations = relations[idx, , drop = FALSE]
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3609
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3610 gR = graph.data.frame(relations,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3611 directed = FALSE,
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3612 vertices = nodes)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3613
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3614 # On supprime les noeuds qui n'ont pas d'arêtes.
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3615 gR = delete.vertices(gR, which(degree(gR) == 0))
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3616
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3617 res = list(gR = gR)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3618 res$cutoff = cutoff
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3619
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3620 return(res)
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3621
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3622
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3623 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3624
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3625
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3626 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3627
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3628
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3629
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3630
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3631 }
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3632
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3633
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3634
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3635
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3636
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3637
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3638
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3639
0a3c83f2197a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 24b8259494ac7ab10cbd1f9ee991f455a7507590-dirty
ppericard
parents:
diff changeset
3640