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planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
author vmarcon
date Thu, 18 Jan 2018 07:44:37 -0500
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1 ###########################################################################
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2 # Quality controls and descriptive analysis plots #
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3 ###########################################################################
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4 # Authors: Melanie Petera #
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5 ###########################################################################
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6 # Description : This script allows various displays of data for quality #
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7 # control and descriptive analysis. The input data is a matrix of #
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8 # quantitative variables, and it returns chosen plots in png format #
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9 # and a table with chosen statistics. #
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10 ###########################################################################
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11 # Specific R packages: #
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12 # - edgeR (needed for MA plots) #
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13 ###########################################################################
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14 # Version 1 (06-06-2014): display boxplot, histogram, density plot, #
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15 # MA plot, pairs plot, and return a table of chosen statistics #
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16 # (quantiles, mean, variance, standard error of the mean) #
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17 ###########################################################################
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18
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19 desc_fct <- function(file.in, nacode, table_file, graph_file, stat, chosen.stat, ploting, chosen.plot, log_file){
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20 # Parameters:
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21 # - file.in: count matrix input (tab-separated) [file name]
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22 # - nacode: missing value coding character
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23 # - table_file: results file containing table of chosen statistics [file name]
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24 # - graph_file: pdf file containing plots for chosen statistics [file name]
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25 # - stat: should statistics be calculated? (TRUE/FALSE)
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26 # - chosen.stat: character listing the chosen statistics (comma-separated)
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27 # - ploting: should graphics be displayed? (TRUE/FALSE)
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28 # - chosen.plot: character listing the chosen plots (comma-separated)
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29 # - log_file: a log file [file name]
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30
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31
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32 ##########################################################
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33 # Read and verify data - - - - - - - - - - - -
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34 # Checks valids for all modules
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35
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36 library(methods)
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37
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38 log_error=function(message="") {
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39 line_use="line"
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40 column_use="column"
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41
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42 cat("<HTML><HEAD><TITLE>Normalization report</TITLE></HEAD><BODY>\n",file=log_file,append=F,sep="")
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43 cat("&#9888 An error occurred while trying to read your table.\n<BR>",file=log_file,append=T,sep="")
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44 cat("Please check that:\n<BR>",file=log_file,append=T,sep="")
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45 cat("<UL>\n",file=log_file,append=T,sep="")
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46 cat(" <LI> the table you want to process contains the same number of columns for each line</LI>\n",file=log_file,append=T,sep="")
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47 cat(" <LI> the first line of your table is a header line (specifying the name of each ",column_use,")</LI>\n",file=log_file,append=T,sep="")
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48 cat(" <LI> the first column of your table specifies the name of each ",line_use,"</LI>\n",file=log_file,append=T,sep="")
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49 cat(" <LI> both individual and variable names should be unique</LI>\n",file=log_file,append=T,sep="")
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50 cat(" <LI> each value is separated from the other by a <B>TAB</B> character</LI>\n",file=log_file,append=T,sep="")
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51 cat(" <LI> except for first line and first column, table should contain a numeric value</LI>\n",file=log_file,append=T,sep="")
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52 cat(" <LI> this value may contain character '.' as decimal separator or '",nacode,"' for missing values</LI>\n",file=log_file,append=T,sep="")
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53 cat("</UL>\n",file=log_file,append=T,sep="")
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54 cat("-------<BR>\nError messages recieved:<BR><FONT color=red>\n",conditionMessage(message),"</FONT>\n",file=log_file,append=T,sep="")
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55 cat("</BODY></HTML>\n",file=log_file,append=T,sep="")
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56 q(save="no",status=1)
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57 }
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58
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59 tab_in=tryCatch(
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60 {
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61 tab_in=read.table(file.in,header=TRUE,na.strings=nacode,sep="\t",check.names=FALSE,quote="\"")
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62 },
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63 error=function(cond) {
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64 log_error(message=cond)
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65 return(NA)
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66 },
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67 warning=function(cond) {
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68 log_error(message=cond)
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69 return(NA)
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70 },
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71 finally={
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72 #Do nothing special
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73 }
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74 )
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75
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76 if (ncol(tab_in)<2) {
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77 log_error(simpleCondition("The table you want to use contains less than two columns."))
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78 }
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79
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80 rn=as.character(tab_in[,1])
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81 if (length(rn)!=length(unique(rn))) {
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82 duplicated_rownames=table(rn)
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83 duplicated_rownames=duplicated_rownames[duplicated_rownames>1]
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84 duplicated_rownames=names(duplicated_rownames)
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85 if (length(duplicated_rownames)>3) {
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86 duplicated_rownames=c(duplicated_rownames[1:3],"...")
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87 }
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88 duplicated_rownames=paste(duplicated_rownames,collapse=", ")
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89 log_error(simpleCondition(
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90 paste("The table you want to use have duplicated values in the first column (",
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91 " - duplicated names: ",duplicated_rownames,sep="")
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92 ))
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93 }
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94 tab=tab_in[,-1]
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95 rownames(tab)=rn
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96
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97 #Check all columns are numerical
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98 tab=as.matrix(tab)
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99 cell.with.na=c()
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100 for (i in 1:ncol(tab)) {
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101 na.v1=is.na(tab[,i])
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102 na.v2=is.na(as.numeric(tab[,i]))
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103 if (sum(na.v1)!=sum(na.v2)) {
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104 sel=which(na.v1!=na.v2)
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105 sel=sel[1]
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106 value=tab[sel,i]
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107 log_error(simpleCondition(
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108 paste("Column '",colnames(tab)[i],"' of your table contains non numerical values. Please check its content (on line #",sel,": value='",value,"').",sep="")
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109 ))
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110 }
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111 if (length(cell.with.na)==0 & sum(na.v1)!=0) {
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112 cell.with.na=c(i,which(na.v1)[1])
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113 }
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114 }
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115
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116 Dataset <- tab_in
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117
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118 ##########################################################
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119 # Statistics table computation - - - - - - - - -
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120
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121 log=""
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122
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123 if(stat=="T" & length(chosen.stat)!=0){
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124
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125 stat.list <- strsplit(chosen.stat,",")[[1]]
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126 stat.res <- t(Dataset[0,,drop=FALSE])
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127
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128 numdig <- 5
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129
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130 if("mean" %in% stat.list){
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131 stat.res <- cbind(stat.res,c("Mean",round(colMeans(Dataset[,-1],na.rm=TRUE),digits=numdig)))
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132 }
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133
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134 if("sd" %in% stat.list){
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135 colSd <- apply(Dataset[,-1],2,sd,na.rm=TRUE)
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136 stat.res <- cbind(stat.res,c("Std.Dev",round(colSd,digits=numdig)))
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137 }
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138
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139 if("variance" %in% stat.list){
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140 colVar <- apply(Dataset[,-1],2,var,na.rm=TRUE)
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141 stat.res <- cbind(stat.res,c("Variance",round(colVar,digits=numdig)))
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142 }
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143
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144 if(("median" %in% stat.list)&&(!("quartile" %in% stat.list))){
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145 colMed <- apply(Dataset[,-1],2,median,na.rm=TRUE)
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146 stat.res <- cbind(stat.res,c("Median",round(colMed,digits=numdig)))
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147 }
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148
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149 if("quartile" %in% stat.list){
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150 colQ <- round(apply(Dataset[,-1],2,quantile,na.rm=TRUE),digits=numdig)
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151 stat.res <- cbind(stat.res,c("Min",colQ[1,]),c("Q1",colQ[2,]),
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152 c("Median",colQ[3,]),c("Q3",colQ[4,]),c("Max",colQ[5,]))
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153 }
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154
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155 if("decile" %in% stat.list){
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156 colD <- round(t(apply(Dataset[,-1],2,quantile,na.rm=TRUE,seq(0,1,0.1))),digits=numdig)
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157 colD <- rbind(paste("D",seq(0,10,1),sep=""),colD)
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158 stat.res <- cbind(stat.res,colD)
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159 }
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160
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161 write.table(stat.res,table_file,col.names=FALSE,sep="\t",quote=FALSE)
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162
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163 log=paste(log,"&#10132; You choose to compute :",chosen.stat,"<BR>")
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164
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165 } # end if(stat)
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166 else{
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167 log=paste(log,"&#10132; You don't choose any stats<BR>")
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168 }
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169
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170 ##########################################################
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171 # Graphics generation - - - - - - - - - - - - -
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172
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173 if(ploting=="T" & length(chosen.plot)!=0){
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174
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175 nb_graph_per_row=4
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176 nb_graph=ncol(Dataset)-1
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177
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178 nb_row=round(nb_graph/nb_graph_per_row)
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179
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180 nb_empty_plot=nb_graph %% nb_graph_per_row
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181 if (nb_empty_plot != 0) {
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182 nb_row=nb_row+1
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183 }
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184
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185 page_height=3.5 * nb_row
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186
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187 pdf(file=graph_file,height=page_height)
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188
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189 graph.list <- strsplit(chosen.plot,",")[[1]]
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190
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191 #For the pair plot, we stick to the default layout
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192 if("pairsplot" %in% graph.list){
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193 pairs(Dataset[,-1])
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194 }
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195
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196 #For the other plots, we have 4 plots per line
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197 par(mfrow=c(nb_row,nb_graph_per_row),mar=c(3, 3, 3, 1) + 0.1)
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198
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199 if("boxplot" %in% graph.list){
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200 for(ech in 2:ncol(Dataset)){
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201 boxplot(Dataset[,ech],main=colnames(Dataset)[ech],xlab=NULL)
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202 }
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203 #Complete page with empty plots
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204 i=0; while (i<nb_empty_plot) {plot.new();i=i+1;}
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205 }
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206
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207 if("histogram" %in% graph.list){
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208 for(ech in 2:ncol(Dataset)){
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209 hist(Dataset[,ech],main=colnames(Dataset)[ech],xlab=NULL)
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210 }
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211 #Complete page with empty plots
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212 i=0; while (i<nb_empty_plot) {plot.new();i=i+1;}
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213 }
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214
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215 if("density" %in% graph.list){
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216 for(ech in 2:ncol(Dataset)){
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217 plot(density(Dataset[,ech],na.rm=TRUE),main=colnames(Dataset)[ech])
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218 }
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219 #Complete page with empty plots
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220 i=0; while (i<nb_empty_plot) {plot.new();i=i+1;}
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221 }
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222
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223
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224 if("MAplot" %in% graph.list){
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225 if(min(Dataset[,-1],na.rm=TRUE)<0){
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226 cat("\n----\nError: MAplot only available for positive variables\n----",file=log_file,append=T,sep="")
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227 q(save="no",status=1)
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228 }
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229 library(limma)
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230
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231 library(edgeR) #Warning : Import also limma package
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232 for(ech in 2:(ncol(Dataset)-1)){
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233 for(ech2 in (ech+1):ncol(Dataset)){
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234 temp.pair <- na.omit(Dataset[,c(ech,ech2)])
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235 maPlot(temp.pair[,1],temp.pair[,2],main=paste(colnames(Dataset)[ech],"VS",colnames(Dataset)[ech2]))
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236 }
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237 }
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238 #Do not complete page with empty plots for this plot because it generates nb_variables X nb_variables graphs
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239 }
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240
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241 #Close pdf device
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242 dev.off()
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243
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244 log=paste(log,"&#10132; You choose to plot :",chosen.plot,"<BR>")
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245 } # end if(ploting)
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246 else{
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247 log=paste(log,"&#10132; You don't choose any plot<BR>")
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248 }
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249
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250
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251
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252 ##########################################################
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253 # Treatment successfull
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254 ##########################################################
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255 cat("<HTML><HEAD><TITLE>Summary statistics report</TITLE></HEAD><BODY>\n",file=log_file,append=F,sep="")
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256 cat(log,file=log_file,append=T,sep="")
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257 cat("&#10003; Your process is successfull!<BR>",file=log_file,append=T,sep="")
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258 cat("</BODY></HTML>\n",file=log_file,append=T,sep="")
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259
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260
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261 } # end of function
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262
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263