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annotate heatmap_viz.R @ 0:00960579bcd3 draft default tip

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planemo upload commit 004439cca3c2fd3b5132eff246d846e5050bfd4f-dirty
author proteore
date Tue, 28 Aug 2018 10:37:03 -0400
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1 #!/usr/bin/Rscript
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2
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3 suppressMessages(library('plotly'))
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4 suppressMessages(library('heatmaply'))
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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
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31 Example:
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32 ./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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33
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34 q(save="no")
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35 }
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36
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37 #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/pathview/args.Rda")
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38 #load("/home/dchristiany/proteore_project/ProteoRE/tools/pathview/args.Rda")
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39 parseArgs <- function(x) strsplit(sub("^--", "", x), "=")
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40 argsDF <- as.data.frame(do.call("rbind", parseArgs(args)))
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41 args <- as.list(as.character(argsDF$V2))
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42 names(args) <- argsDF$V1
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43
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44 return(args)
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45 }
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46
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47 read_file <- function(path,header){
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48 file <- try(read.table(path,header=header, sep="\t",stringsAsFactors = FALSE, quote=""),silent=TRUE)
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49 if (inherits(file,"try-error")){
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50 stop("File not found !")
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51 }else{
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52 return(file)
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53 }
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54 }
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55
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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 args <- get_args()
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67 header=str2bool(args$header)
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68 output <- rapply(strsplit(args$output,"\\."),c) #remove extension
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69 output <- paste(output[1:length(output)-1],collapse=".")
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70 output <- paste(output,args$type,sep=".")
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71 first_col=as.numeric(substr(args$cols,1,1))
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72 last_col=as.numeric(substr(args$cols,3,3))
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73
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74 ###save and load args in rda file for testing
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75 #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/heatmap_viz/args.Rda")
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76 #load("/home/dchristiany/proteore_project/ProteoRE/tools/heatmap_viz/args.Rda")
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77
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78
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79 uto <- read_file(args$input,header = header)
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80 uto_light <- uto[,first_col:last_col]
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81 rownames(uto_light) <- uto[,as.numeric(args$row_names)]
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82 colnames(uto_light) <- sapply(colnames(uto_light),function(x) gsub("iBAQ_","",x),USE.NAMES = FALSE)
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83
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84 if (header) {
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85 heatmaply(uto_light, file=output, margins=c(100,50,NA,0), plot_method="plotly", labRow = rownames(uto_light), labCol = names(uto_light),
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86 grid_gap = 0,cexCol = 1, column_text_angle = as.numeric(args$col_text_angle), width = 1000, height=1000, colors = c('blue','green','yellow','red'))
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87 }else{
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88 names(uto_light) <-c(first_col:last_col)
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89 heatmaply(uto_light, file=output, margins=c(100,50,NA,0), plot_method="plotly", labRow = rownames(uto_light),
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90 grid_gap = 0,cexCol = 1, column_text_angle = as.numeric(args$col_text_angle), width = 1000, height=1000, colors = c('blue','green','yellow','red'))
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91 }
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92
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93
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94 #write.table(uto_light, file = "uto_light.tsv",sep="\t",row.names = FALSE)
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95
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96 ####heatmaply
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97
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98 simulateExprData <- function(n, n0, p, rho0, rho1){
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99 # n: total number of subjects
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100 # n0: number of subjects with exposure 0
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101 # n1: number of subjects with exposure 1
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102 # p: number of genes
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103 # rho0: rho between Z_i and Z_j for subjects with exposure 0
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104 # rho1: rho between Z_i and Z_j for subjects with exposure 1
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105
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106 # Simulate gene expression values according to exposure 0 or 1,
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107 # according to a centered multivariate normal distribution with
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108 # covariance between Z_i and Z_j being rho^|i-j|
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109 n1 <- n - n0
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110 times <- 1:p
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111 H <- abs(outer(times, times, "-"))
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112 V0 <- rho0^H
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113 V1 <- rho1^H
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114
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115 # rows are people, columns are genes
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116 genes0 <- MASS::mvrnorm(n = n0, mu = rep(0,p), Sigma = V0)
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117 genes1 <- MASS::mvrnorm(n = n1, mu = rep(0,p), Sigma = V1)
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118 genes <- rbind(genes0,genes1)
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119 return(genes)
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120 }
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121
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122 #genes <- simulateExprData(n = 50, n0 = 25, p = 100, rho0 = 0.01, rho1 = 0.95)
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123
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124 #heatmaply(genes, k_row = 2, k_col = 2)
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125
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126 #heatmaply(cor(genes), k_row = 2, k_col = 2)
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