annotate heatmap_viz.R @ 0:edbb84a94a36 draft

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author proteore
date Tue, 18 Dec 2018 09:58:49 -0500
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children b8a5139cf5b9
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 #!/usr/bin/Rscript
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2
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3 suppressMessages(library('plotly',quietly = T))
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4 suppressMessages(library('heatmaply',quietly = T))
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5
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6 #packageVersion('plotly')
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7
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8 get_args <- function(){
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9
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10 ## Collect arguments
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11 args <- commandArgs(TRUE)
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12
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13 ## Default setting when no arguments passed
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14 if(length(args) < 1) {
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15 args <- c("--help")
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16 }
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17
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18 ## Help section
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19 if("--help" %in% args) {
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20 cat("Pathview R script
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21 Arguments:
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22 --help Print this test
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23 --input path of the input file (must contains a colum of uniprot and/or geneID accession number)
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24 --output Output file
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25 --type type of output file, could be html, pdf, jpg or png
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26 --cols Columns to use for heatmap, exemple : '3:8' to use columns from the third to the 8th
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27 --row_names Column which contains row names
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28 --header True or False
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29 --col_text_angle Angle of columns label ; from -90 to 90 degres
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30 --dist_fun function used to compute the distance
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31
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32 Example:
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33 ./heatmap_viz.R --input='dat.nucl.norm.imputed.tsv' --output='heatmap.html' --cols='3:8' --row_names='2' --header=TRUE --col_text_angle=0 \n\n")
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34
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35 q(save="no")
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36 }
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37
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38 parseArgs <- function(x) strsplit(sub("^--", "", x), "=")
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39 argsDF <- as.data.frame(do.call("rbind", parseArgs(args)))
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40 args <- as.list(as.character(argsDF$V2))
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41 names(args) <- argsDF$V1
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42
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43 return(args)
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44 }
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45
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46 read_file <- function(path,header){
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47 file <- try(read.csv(path,header=header, sep="\t",stringsAsFactors = FALSE, quote="",fill=TRUE,check.names = F),silent=TRUE)
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48 if (inherits(file,"try-error")){
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49 stop("File not found !")
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50 }else{
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51 return(file)
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52 }
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53 }
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54
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55 #convert a string to boolean
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56 str2bool <- function(x){
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57 if (any(is.element(c("t","true"),tolower(x)))){
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58 return (TRUE)
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59 }else if (any(is.element(c("f","false"),tolower(x)))){
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60 return (FALSE)
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61 }else{
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62 return(NULL)
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63 }
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64 }
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65
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66 #remove remaining quote
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67 #only keep usefull columns
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68 #remove lines with at least one empty cell in a matrix between two defined columns
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69 clean_df <- function(mat,cols,rownames_col){
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70 uto = mat[,cols]
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71 uto <- as.data.frame(apply(uto,c(1,2),function(x) gsub(",",".",x)))
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72 uto <- as.data.frame(apply(uto,c(1,2),function(x) {ifelse(is.character(x),as.numeric(x),x)}))
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73 rownames(uto) <- mat[,rownames_col]
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74 #bad_lines <- which(apply(uto, 1, function(x) any(is.na(x))))
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75 #if (length(bad_lines) > 0) {
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76 # uto <- uto[- bad_lines,]
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77 # print(paste("lines",bad_lines, "has been removed: at least one non numeric content"))
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78 #}
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79 return(uto)
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80 }
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81
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82 get_cols <-function(input_cols) {
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83 input_cols <- gsub("c","",input_cols)
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84 if (grepl(":",input_cols)) {
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85 first_col=unlist(strsplit(input_cols,":"))[1]
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86 last_col=unlist(strsplit(input_cols,":"))[2]
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87 cols=first_col:last_col
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88 } else {
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89 cols = as.integer(unlist(strsplit(input_cols,",")))
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90 }
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91 return(cols)
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92 }
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93
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94 #get args
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95 args <- get_args()
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96
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97 #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/heatmap_viz/args.rda")
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98 #load("/home/dchristiany/proteore_project/ProteoRE/tools/heatmap_viz/args.rda")
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99
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100 header=str2bool(args$header)
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101 output <- rapply(strsplit(args$output,"\\."),c) #remove extension
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102 output <- paste(output[1:length(output)-1],collapse=".")
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103 output <- paste(output,args$type,sep=".")
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104 cols = get_cols(args$cols)
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105 rownames_col = as.integer(gsub("c","",args$row_names))
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106 if (length(cols) <=1 ){
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107 stop("You need several colums to build a heatmap")
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108 }
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109 dist=args$dist
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110 clust=args$clust
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111 dendrogram=args$dendrogram
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112
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113 #cleaning data
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114 uto <- read_file(args$input,header)
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115 uto <- clean_df(uto,cols,rownames_col)
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116 uto <- uto[rowSums(is.na(uto)) != ncol(uto), ] #remove emptylines
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117
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118 if (header) {
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119 col_names = names(data)
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120 } else {
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121 col_names = cols
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122 }
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123
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124 #building heatmap
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125 if (dist %in% c("pearson","spearman","kendall")){
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126 heatmaply(uto, file=output, margins=c(100,50,NA,0), plot_method="plotly", labRow = rownames(uto), labCol = col_names, distfun=dist,
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127 hclust_method = clust, dendrogram = dendrogram, grid_gap = 0,cexCol = 1, column_text_angle = as.numeric(args$col_text_angle),
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128 width = 1000, height=1000, colors = c('blue','green','yellow','red'))
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129 } else {
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130 heatmaply(uto, file=output, margins=c(100,50,NA,0), plot_method="plotly", labRow = rownames(uto), labCol = col_names, dist_method = dist,
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131 hclust_method = clust, dendrogram = dendrogram, grid_gap = 0,cexCol = 1, column_text_angle = as.numeric(args$col_text_angle),
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132 width = 1000, height=1000, colors = c('blue','green','yellow','red'))
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133 }
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134
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135 ####heatmaply
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136
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137 simulateExprData <- function(n, n0, p, rho0, rho1){ row
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138 # n: total number of subjects
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139 # n0: number of subjects with exposure 0
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140 # n1: number of subjects with exposure 1
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141 # p: number of genes
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142 # rho0: rho between Z_i and Z_j for subjects with exposure 0
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143 # rho1: rho between Z_i and Z_j for subjects with exposure 1
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144
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145 # Simulate gene expression values according to exposure 0 or 1,
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146 # according to a centered multivariate normal distribution with
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147 # covariance between Z_i and Z_j being rho^|i-j|
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148 n1 <- n - n0
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149 times <- 1:p
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150 H <- abs(outer(times, times, "-"))
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151 V0 <- rho0^H
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152 V1 <- rho1^H
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153
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154 # rows are people, columns are genes
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155 genes0 <- MASS::mvrnorm(n = n0, mu = rep(0,p), Sigma = V0)
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156 genes1 <- MASS::mvrnorm(n = n1, mu = rep(0,p), Sigma = V1)
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157 genes <- rbind(genes0,genes1)
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158 return(genes)
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159 }
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160
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161 #genes <- simulateExprData(n = 50, n0 = 25, p = 100, rho0 = 0.01, rho1 = 0.95)
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162
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163 #heatmaply(genes, k_row = 2, k_col = 2)
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164
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165 #heatmaply(cor(genes), k_row = 2, k_col = 2)
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166
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167
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168
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169
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170
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171
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172