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1 # Density Plot Module for Galaxy
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2 # ggplot2
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3 ######################################################################
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4 # Copyright (c) 2016 Northrop Grumman.
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5 # All rights reserved.
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6 ######################################################################
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7 #
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8 # Version 1
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9 # Cristel Thomas
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10 #
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11 #
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12
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13 library(ggplot2)
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14 library(grid)
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15 # Multiple plot function
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16 # from http://www.cookbook-r.com/Graphs/Multiple_graphs_on_one_page_%28ggplot2%29/
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17 # ggplot objects can be passed in ..., or to plotlist (as a list of ggplot objects)
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18 # - cols: Number of columns in layout
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19 # - layout: A matrix specifying the layout. If present, 'cols' is ignored.
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20 #
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21 # If the layout is something like matrix(c(1,2,3,3), nrow=2, byrow=TRUE),
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22 # then plot 1 will go in the upper left, 2 will go in the upper right, and
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23 # 3 will go all the way across the bottom.
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24 #
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25 multiplot <- function(..., plotlist=NULL, file, cols=1, layout=NULL) {
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26 # Make a list from the ... arguments and plotlist
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27 plots <- c(list(...), plotlist)
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28 numPlots = length(plots)
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29
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30 # If layout is NULL, then use 'cols' to determine layout
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31 if (is.null(layout)) {
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32 # Make the panel
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33 # ncol: Number of columns of plots
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34 # nrow: Number of rows needed, calculated from # of cols
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35 layout <- matrix(seq(1, cols * ceiling(numPlots/cols)),
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36 ncol = cols, nrow = ceiling(numPlots/cols))
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37 }
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38
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39 if (numPlots==1) {
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40 print(plots[[1]])
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41 } else {
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42 # Set up the page
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43 grid.newpage()
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44 pushViewport(viewport(layout = grid.layout(nrow(layout), ncol(layout))))
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45
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46 # Make each plot, in the correct location
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47 for (i in 1:numPlots) {
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48 # Get the i,j matrix positions of the regions that contain this subplot
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49 matchidx <- as.data.frame(which(layout == i, arr.ind = TRUE))
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50 print(plots[[i]], vp = viewport(layout.pos.row = matchidx$row,
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51 layout.pos.col = matchidx$col))
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52 }
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53 }
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54 }
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55
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56 generateGraphFromText <- function(input, channels, output, plot_default, flag_pdf, pdf_out) {
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57 fcs <- read.table(input, header = TRUE, sep = "\t", check.names = FALSE)
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58 ## marker names
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59 markers <- colnames(fcs)
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60
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61 if (plot_default) {
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62 channels <- c(grep(colnames(fcs), pattern="Forward scatter", ignore.case=TRUE),
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63 grep(colnames(fcs), pattern="Side scatter", ignore.case=TRUE))
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64 if (length(channels) == 0){
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65 channels <- c(grep(colnames(fcs), pattern="FSC"),
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66 grep(colnames(fcs), pattern="SSC"))
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67 if (length(channels) > 2) {
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68 #get first FSC and corresponding SSC
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69 channels <- c(grep(colnames(fcs), pattern="FSC-A"),
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70 grep(colnames(fcs), pattern="SSC-A"))
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71 if (length(channels) == 0) {
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72 channels <- c(grep(colnames(fcs), pattern="FSC-H"),
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73 grep(colnames(fcs), pattern="SSC-H"))
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74 if (length(channels) == 0) {
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75 channels <- c(grep(colnames(fcs), pattern="FSC-W"),
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76 grep(colnames(fcs), pattern="SSC-W"))
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77 }
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78 }
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79 }
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80 }
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81 if (length(channels) == 0) {
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82 warning('No forward/side scatter channels found, no plots will be generated.')
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83 quit(save = "no", status = 10, runLast = FALSE)
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84 }
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85 }
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86
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87 nb_markers <- length(channels)
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88
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89 for (j in nb_markers) {
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90 if (channels[j] > length(markers)){
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91 warning('Please indicate markers between 1 and ', length(markers))
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92 quit(save = "no", status = 10, runLast = FALSE)
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93 }
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94 }
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95
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96 plots <- list()
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97 i <- 0
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98 for (m in 1:(nb_markers - 1)) {
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99 for (n in (m+1):nb_markers) {
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100 x <- fcs[,channels[m]]
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101 y <- fcs[,channels[n]]
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102 df <- data.frame(x = x, y = y,
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103 d = densCols(x, y, colramp = colorRampPalette(rev(rainbow(10, end = 4/6)))))
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104 p <- ggplot(df) +
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105 geom_point(aes(x, y, col = d), size = 0.2) +
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106 scale_color_identity() +
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107 theme_bw() +
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108 labs(x = markers[channels[m]]) +
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109 labs(y = markers[channels[n]])
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110 i <- i + 1
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111 plots[[i]] <- p
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112 }
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113 }
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114 png(output, type="cairo", width=800, height=800)
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115 multiplot(plotlist = plots, cols = 2)
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116 dev.off()
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117 if (flag_pdf){
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118 pdf(pdf_out, useDingbats=FALSE, onefile=TRUE)
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119 multiplot(plotlist = plots, cols = 2)
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120 dev.off()
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121 }
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122 }
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123
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124 args <- commandArgs(trailingOnly = TRUE)
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125 channels <- ""
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126 flag_default <- FALSE
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127 flag_pdf <- FALSE
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128 pdf_output <- ""
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129
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130 if (args[3]=="None") {
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131 flag_default <- TRUE
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132 } else {
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133 if (args[3] == "i.e.:1,3,4"){
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134 flag_default <- TRUE
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135 } else {
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136 channels <- as.numeric(strsplit(args[3], ",")[[1]])
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137 for (channel in channels){
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138 if (is.na(channel)){
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139 quit(save = "no", status = 11, runLast = FALSE)
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140 }
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141 }
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142 if (length(channels) == 1){
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143 warning('Please indicate more than one marker to plot.')
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144 quit(save = "no", status = 10, runLast = FALSE)
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145 }
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146 }
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147 }
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148
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149 if (args[5] == "TRUE"){
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150 pdf_output <- args[6]
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151 flag_pdf <- TRUE
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152 }
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153 generateGraphFromText(args[2], channels, args[4], flag_default, flag_pdf, pdf_output)
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