Mercurial > repos > gaelcge > r_signac_galaxy

annotate signac-vlnplot.R @ 0:6e0b320d8b6a draft default tip

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"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
author gaelcge
date Tue, 02 Aug 2022 19:11:27 +0000
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1 #!/usr/bin/env Rscript
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2
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3 # Load optparse we need to check inputs
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4
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5 suppressPackageStartupMessages(require(optparse))
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6
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7 # Load common functions
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8
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9 suppressPackageStartupMessages(require(workflowscriptscommon))
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10
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11 # parse options
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12
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13 option_list = list(
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14 make_option(
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15 c("--signac-object"),
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16 action = "store",
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17 default = NA,
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18 type = 'character',
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19 help = ""
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20 ),
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21 make_option(
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22 c("--features"),
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23 action = "store",
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24 default = NA,
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25 type = 'character',
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26 help = "File to be used to derive a vector of genes to test."
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27 ),
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28 make_option(
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29 c("--cols"),
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30 action = "store",
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31 default = NULL,
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32 type = 'character',
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33 help = "File to be used to derive a vector of colors."
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34 ),
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35 make_option(
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36 c("-p", "--pt-size"),
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37 action = "store",
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38 default = 1,
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39 type = 'integer',
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40 help = "Adjust point size for plotting."
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41 ),
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42 make_option(
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43 c("--group-by"),
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44 action = "store",
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45 default = "ident",
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46 type = 'character',
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47 help = "Group (color) cells in different ways (for example, orig.ident)."
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48 ),
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49 make_option(
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50 c("--sort"),
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51 action = "store",
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52 type = 'logical',
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53 help = "Sort identity classes (on the x-axis) by the average expression of the attribute being potted, can also pass 'increasing' or 'decreasing' to change sort direction."
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54 ),
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55 make_option(
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56 c("--assay"),
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57 action = "store",
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58 default = NULL,
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59 type = 'character',
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60 help = "Name of assay to use, defaults to the active assay."
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61 ),
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62 # make_option(
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63 # c("--split-by"),
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64 # action = "store",
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65 # default = NULL,
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66 # type = 'character',
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67 # help = "A variable to split the violin plots by."
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68 # ),
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69 make_option(
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70 c("--same-y-lims"),
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71 action = "store",
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72 default = FALSE,
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73 type = 'logical',
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74 help = "Set all the y-axis limits to the same values."
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75 ),
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76 make_option(
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77 c("--log"),
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78 action = "store",
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79 default = FALSE,
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80 type = 'logical',
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81 help = "plot the feature axis on log scale."
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82 ),
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83 make_option(
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84 c("--ncol"),
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85 action = "store",
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86 default = NULL,
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87 type = 'integer',
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88 help = "Number of columns if multiple plots are displayed."
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89 ),
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90 make_option(
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91 c("--slot"),
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92 action = "store",
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93 default = 'data',
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94 type = 'character',
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95 help = "Use non-normalized counts data for plotting."
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96 ),
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97 # make_option(
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98 # c("--split-plot"),
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99 # action = "store",
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100 # default = FALSE,
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101 # type = 'logical',
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102 # help = "plot each group of the split violin plots by multiple or single violin shapes."
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103 # ),
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104 make_option(
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105 c("--stack"),
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106 action = "store",
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107 default = FALSE,
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108 type = 'logical',
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109 help = "Horizontally stack plots for each feature."
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110 ),
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111 make_option(
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112 c("--fill-by"),
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113 action = "store",
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114 default = 'feature',
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115 type = 'character',
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116 help = "Color violins/ridges based on either 'feature' or 'ident'."
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117 ),
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118 make_option(
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119 c("--flip"),
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120 action = "store",
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121 default = FALSE,
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122 type = 'logical',
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123 help = "flip plot orientation (identities on x-axis)."
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124 ),
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125 make_option(
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126 c("--png-width"),
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127 action = "store",
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128 default = 1000,
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129 type = 'integer',
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130 help = "Width of png (px)."
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131 ),
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132 make_option(
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133 c("--png-height"),
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134 action = "store",
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135 default = 1000,
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136 type = 'integer',
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137 help = "Height of png file (px)."
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138 ),
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139 make_option(
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140 c("--output_image_file"),
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141 action = "store",
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142 default = NA,
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143 type = 'character',
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144 help = "File name in which to store serialized R matrix object."
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145 )
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146 )
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147
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148 opt <- wsc_parse_args(option_list)
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149
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150 suppressPackageStartupMessages(require(Seurat))
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151 suppressPackageStartupMessages(require(Signac))
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152
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153 set.seed(1234)
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154
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155 if (! file.exists(opt$signac_object)){
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156 stop((paste('File', opt$signac_object, 'does not exist')))
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157 }
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158
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159 # Check features
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160 features <- NULL
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161 if (! is.null(opt$features) && opt$features != 'NULL'){
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162 features <- strsplit(opt$features, ",")[[1]]
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163 }
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164
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165 # Check cols
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166 cols <- NULL
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167 if (! is.null(opt$cols) && opt$cols != 'NULL'){
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168 if (! file.exists(opt$cols)){
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169 stop((paste('Supplied features file', opt$cols, 'does not exist')))
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170 }else{
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171 cols <- readLines(opt$cols)
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172 }
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173 }
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174
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175 # Check assay
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176 assay <- NULL
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177 if (! is.null(opt$assay) && opt$assay != 'NULL'){
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178 assay <- opt$assay
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179 }
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180
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181 # extract gene annotations from EnsDb
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182 signac_object <- readRDS(file = opt$signac_object)
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183
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184 group_by <- if(opt$group_by == 'ident'){
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185 NULL
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186 }else{
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187 opt$group_by
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188 }
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189
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190 # sort <- if(opt$sort == 'False'){
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191 # FALSE
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192 # }else{
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193 # TRUE
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194 # }
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195
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196 png(filename = opt$output_image_file, width = opt$png_width, height = opt$png_height)
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197 VlnPlot(object = signac_object,
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198 features = features,
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199 cols = cols,
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200 pt.size = opt$pt_size,
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201 group.by = group_by,
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202 sort = opt$sort,
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203 assay = assay,
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204 #split.by = opt$split_by,
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205 same.y.lims = opt$same_y_lims,
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206 log = opt$log,
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207 ncol = opt$ncol,
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208 slot = opt$slot,
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209 #split.plot = opt$split_plot,
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210 stack = opt$stack,
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211 fill.by = opt$fill_by,
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212 flip = opt$flip
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213 )
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214 dev.off()