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1 #########################################################################
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2 # SCRIPT INTENSITY CHECK #
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3 # #
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4 # Input: Data Matrix, VariableMetadata, SampleMetadata #
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5 # Output: VariableMetadata, Graphics (barplots and boxplots) #
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6 # #
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7 # Dependencies: RcheckLibrary.R #
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8 # #
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9 #########################################################################
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10
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11
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12 # Parameters (for dev)
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13 if(FALSE){
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14
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15 rm(list = ls())
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16 setwd("Y:\\Developpement\\Intensity check\\Pour tests")
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17
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18 DM.name <- "DM_NA.tabular"
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19 SM.name <- "SM_NA.tabular"
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20 VM.name <- "vM_NA.tabular"
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21 class.col <- "2"
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22 type <- "One_class"
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23 class1 <- "Blanks"
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24 fold.frac <- "Top"
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25 logarithm <- "log2"
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26 VM.output <- "new_VM.txt"
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27 graphs.output <- "Barplots_and_Boxplots.pdf"
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28 }
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29
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30
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31
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32
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33 intens_check <- function(DM.name, SM.name, VM.name, class.col, type, class1, fold.frac, logarithm,
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34 VM.output, graphs.output){
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35
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36
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37 # This function allows to check the intensities considering classes with a mean fold change calculation,
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38 # the number and the proportion of missing values (NA) in dataMatrix
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39 #
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40 # Two options:
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41 # - one class (selected by the user) against all the remaining samples ("One_class")
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42 # - tests on each class ("Each_class")
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43 #
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44 # Parameters:
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45 # DM.name, SM.name, VM.name: dataMatrix, sampleMetadata, variableMetadata files access
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46 # class.col: number of the sampleMetadata's column with classes
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47 # type: "One_class" or "Each_class"
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48 # class1: name of the class, only if type="One_class"
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49 # fold.frac: if type="One class": class1/other ("Top") or other/class1 ("Bottom")
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50 # logarithm: "log2", "log10" or "none" for log mean fold change
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51 # VM.output: output file's access (VM with new columns)
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52 # graphs.output: pdf file's access with barplots for the proportion of NA and boxplots with the folds values
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53
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54
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55
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56
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57
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58 # Input ---------------------------------------------------------------------------------------------------
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59
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60 DM <- read.table(DM.name, header=TRUE, sep="\t", check.names=FALSE)
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61 SM <- read.table(SM.name, header=TRUE, sep="\t", check.names=FALSE)
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62 VM <- read.table(VM.name, header=TRUE, sep="\t", check.names=FALSE)
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63
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64
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65
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66 # Table match check with Rchecklibrary
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67 table.check <- match3(DM, SM, VM)
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68 check.err(table.check)
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69
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70
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71
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72 rownames(DM) <- DM[,1]
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73 var_names <- DM[,1]
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74 DM <- DM[,-1]
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75 DM <- data.frame(t(DM))
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76
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77 class.col <- colnames(SM)[as.numeric(class.col)]
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78
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79
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80 # check class.col, class1 and the number of classes ---------------------------------------------------------
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81
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82 if(!(class.col %in% colnames(SM))){
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83 stop("\n- - - - - - - - -\n", "The column ",class.col, " is not a part of the specify sample Metadata","\n- - - - - - - - -\n")
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84 }
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85
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86 c_class <- SM[,class.col]
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87 c_class <- as.factor(c_class)
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88 nb_class <- nlevels(c_class)
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89 classnames <- levels(c_class)
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90
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91 if(nb_class < 2){
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92 err.1class <- c("\n The column",class.col, "contains only one class, fold calculation could not be executed \n")
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93 cat(err.1class)
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94 }
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95
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96 if((nb_class > (nrow(SM))/3)){
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97 class.err <- c("\n There are too many classes, think about reducing the number of classes and excluding those
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98 with few samples \n")
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99 cat(class.err)
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100 }
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101
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102
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103 if(type == "One_class"){
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104 if(!(class1 %in% classnames)){
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105 list.class1 <- c("\n Classes:",classnames,"\n")
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106 cat(list.class1)
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107 err.class1 <- c("The class ",class1, " does not appear in the column ", class.col)
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108 stop("\n- - - - - - - - -\n", err.class1,"\n- - - - - - - - -\n")
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109 }
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110 }
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111
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112
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113 #If type is "one_class", change others classes in "other"
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114 if(type == "One_class"){
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115 for(i in 1:length(c_class)){
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116 if(c_class[i]!=class1){
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117 c_class <- as.character(c_class)
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118 c_class[i] <- "Other"
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119 c_class <- as.factor(c_class)
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120 nb_class <- nlevels(c_class)
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121 classnames <- c(class1,"Other")
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122
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123 }
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124 }
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125 }
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126
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127 DM <- cbind(DM,c_class)
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128
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129
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130
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131 # fold calculation -------------------------------------------------------------------------------------------
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132
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133 if(nb_class >= 2){
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134
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135
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136 fold <- data.frame()
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137 n <- 1
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138 ratio1 <- NULL
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139 ratio2 <- NULL
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140
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141 if(type=="Each_class"){
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142 fold.frac <- "Top"
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143 }
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144
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145 for(j in 1:(nb_class-1)){
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146 for(k in (j+1):nb_class) {
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147
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148 if(fold.frac=="Bottom"){
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149 ratio1 <- classnames[k]
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150 ratio2 <- classnames[j]
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151 }else{
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152 ratio1 <- classnames[j]
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153 ratio2 <- classnames[k]
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154 }
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155
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156 for (i in 1:(length(DM)-1)){
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157 fold[i,n] <- mean(DM[which(DM$c_class==ratio1),i], na.rm=TRUE)/
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158 mean(DM[which(DM$c_class==ratio2),i], na.rm=TRUE)
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159 if(logarithm=="log2"){
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160 fold[i,n] <- log2(fold[i,n])
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161 }else if(logarithm=="log10"){
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162 fold[i,n] <- log10(fold[i,n])
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163 }
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164 }
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165 names(fold)[n] <- paste("fold",ratio1,"VS", ratio2, sep="_")
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166 if(logarithm != "none"){
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167 names(fold)[n] <- paste(logarithm,names(fold)[n], sep="_")
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168 }
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169 n <- n + 1}
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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 # number and proportion of NA ---------------------------------------------------------------------------------
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175
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176 calcul_NA <- data.frame()
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177 pct_NA <- data.frame()
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178 for (i in 1:(length(DM)-1)){
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179 for (j in 1:nb_class){
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180 n <- 0
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181 new_DM <- DM[which(DM$c_class==classnames[j]),i]
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182 for(k in 1:length(new_DM)){
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183 if (is.na(new_DM[k])){
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184 n <- n + 1}
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185 calcul_NA[i,j] <- n
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186 pct_NA[i,j] <- (calcul_NA[i,j]/length(new_DM))*100}
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187 }
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188 }
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189 names(calcul_NA) <- paste("NA",classnames, sep="_")
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190 names(pct_NA) <- paste("Pct_NA", classnames, sep="_")
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191
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192 # Alert message if there is no NA in data matrix
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193
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194 sumNA <- colSums(calcul_NA)
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195 sum_total <- sum(sumNA)
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196 alerte <- NULL
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197 if(sum_total==0){
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198 alerte <- c(alerte, "Data Matrix contains no NA.\n")
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199 }
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200
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201 if(length(alerte) != 0){
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202 cat(alerte,"\n")
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203 }
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204 table_NA <- cbind(calcul_NA, pct_NA)
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205
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206
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207
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208 # check columns names ---------------------------------------------------------------------------------------
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209
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210
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211 VM.names <- colnames(VM)
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212
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213 # Fold
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214
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215 if(nb_class >=2){
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216 fold.names <- colnames(fold)
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217
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218 for (i in 1:length(VM.names)){
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219 for (j in 1:length(fold.names)){
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220 if (VM.names[i]==fold.names[j]){
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221 fold.names[j] <- paste(fold.names[j],"2", sep="_")
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222 }
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223 }
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224 }
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225 colnames(fold) <- fold.names
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226
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227 VM <- cbind(VM,fold)
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228 }
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229
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230 # NA
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231 NA.names <- colnames(table_NA)
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232
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233 for (i in 1:length(VM.names)){
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234 for (j in 1:length(NA.names)){
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235 if (VM.names[i]==NA.names[j]){
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236 NA.names[j] <- paste(NA.names[j],"2", sep="_")
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237 }
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238 }
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239 }
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240 colnames(table_NA) <- NA.names
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241 VM <- cbind(VM,table_NA)
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242
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243
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244 #for NA barplots -------------------------------------------------------------------------------------------
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245
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246 data_bp <- data.frame()
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247
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248 for (j in 1:ncol(pct_NA)){
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249 Nb_NA_0_20 <- 0
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250 Nb_NA_20_40 <- 0
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251 Nb_NA_40_60 <- 0
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252 Nb_NA_60_80 <- 0
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253 Nb_NA_80_100 <- 0
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254 for (i in 1:nrow(pct_NA)){
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255
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256 if ((0<=pct_NA[i,j])&(pct_NA[i,j]<20)){
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257 Nb_NA_0_20=Nb_NA_0_20+1
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258 }
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259
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260 if ((20<=pct_NA[i,j])&(pct_NA[i,j]<40)){
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261 Nb_NA_20_40=Nb_NA_20_40+1}
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262
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263 if ((40<=pct_NA[i,j])&(pct_NA[i,j]<60)){
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264 Nb_NA_40_60=Nb_NA_40_60+1}
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265
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266 if ((60<=pct_NA[i,j])&(pct_NA[i,j]<80)){
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267 Nb_NA_60_80=Nb_NA_60_80+1}
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268
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269 if ((80<=pct_NA[i,j])&(pct_NA[i,j]<=100)){
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270 Nb_NA_80_100=Nb_NA_80_100+1}
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271 }
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272 data_bp[1,j] <- Nb_NA_0_20
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273 data_bp[2,j] <- Nb_NA_20_40
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274 data_bp[3,j] <- Nb_NA_40_60
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275 data_bp[4,j] <- Nb_NA_60_80
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276 data_bp[5,j] <- Nb_NA_80_100
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277 }
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278 rownames(data_bp) <- c("0%-20%", "20%-40%", "40%-60%", "60%-80%", "80%-100%")
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279 colnames(data_bp) <- classnames
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280 data_bp <- as.matrix(data_bp)
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281
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282
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283 # Output ---------------------------------------------------------------------------------------------------
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284
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285
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286 write.table(VM, VM.output,sep="\t", quote=FALSE, row.names=FALSE)
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287
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288 #graphics pdf
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289
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290 pdf(graphs.output)
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291
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292 #Barplots for NA
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293 par(mar=c(5.1, 4.1, 4.1, 8.1), xpd=TRUE)
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294
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295 bp=barplot(data_bp, col=rainbow(nrow(data_bp)), main="Proportion of NA", xlab="Classes", ylab="Variables")
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296 legend("topright", fill=rainbow(nrow(data_bp)),rownames(data_bp), inset=c(-0.3,0))
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297
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298 stock=0
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299 for (i in 1:nrow(data_bp)){
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300 text(bp, stock+data_bp[i,]/2, data_bp[i,], col="white", cex=0.7)
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301 stock <- stock+data_bp[i,]
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302 }
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303
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304
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305 #Boxplots for fold test
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306
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307 if(nb_class >= 2){
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308
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309 clean_fold <- fold
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310 for(i in 1:nrow(clean_fold)){
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311 for(j in 1:ncol(clean_fold)){
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312 if(is.infinite(clean_fold[i,j])){
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313 clean_fold[i,j] <- NA
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314 }
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315 }
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316 }
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317 for (j in 1:ncol(clean_fold)){
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318 title <- paste(fold.names[j])
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319 boxplot(clean_fold[j], main=title)
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320 }
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321 }
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322
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323 dev.off()
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324
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325 }
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326
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327 |
