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comparison flowtext_scatterplot/getDensityPlots_text.R @ 0:cc2266d3e611 draft

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author immport-devteam
date Mon, 27 Feb 2017 12:58:47 -0500
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1 # Density Plot Module for Galaxy
2 # ggplot2
3 ######################################################################
4 # Copyright (c) 2016 Northrop Grumman.
5 # All rights reserved.
6 ######################################################################
7 #
8 # Version 1
9 # Cristel Thomas
10 #
11 #
12
13 library(ggplot2)
14 library(grid)
15 # Multiple plot function
16 # from http://www.cookbook-r.com/Graphs/Multiple_graphs_on_one_page_%28ggplot2%29/
17 # ggplot objects can be passed in ..., or to plotlist (as a list of ggplot objects)
18 # - cols: Number of columns in layout
19 # - layout: A matrix specifying the layout. If present, 'cols' is ignored.
20 #
21 # If the layout is something like matrix(c(1,2,3,3), nrow=2, byrow=TRUE),
22 # then plot 1 will go in the upper left, 2 will go in the upper right, and
23 # 3 will go all the way across the bottom.
24 #
25 multiplot <- function(..., plotlist=NULL, file, cols=1, layout=NULL) {
26 # Make a list from the ... arguments and plotlist
27 plots <- c(list(...), plotlist)
28 numPlots = length(plots)
29
30 # If layout is NULL, then use 'cols' to determine layout
31 if (is.null(layout)) {
32 # Make the panel
33 # ncol: Number of columns of plots
34 # nrow: Number of rows needed, calculated from # of cols
35 layout <- matrix(seq(1, cols * ceiling(numPlots/cols)),
36 ncol = cols, nrow = ceiling(numPlots/cols))
37 }
38
39 if (numPlots==1) {
40 print(plots[[1]])
41 } else {
42 # Set up the page
43 grid.newpage()
44 pushViewport(viewport(layout = grid.layout(nrow(layout), ncol(layout))))
45
46 # Make each plot, in the correct location
47 for (i in 1:numPlots) {
48 # Get the i,j matrix positions of the regions that contain this subplot
49 matchidx <- as.data.frame(which(layout == i, arr.ind = TRUE))
50 print(plots[[i]], vp = viewport(layout.pos.row = matchidx$row,
51 layout.pos.col = matchidx$col))
52 }
53 }
54 }
55
56 generateGraphFromText <- function(input, channels, output, plot_default, flag_pdf, pdf_out) {
57 fcs <- read.table(input, header = TRUE, sep = "\t", check.names = FALSE)
58 ## marker names
59 markers <- colnames(fcs)
60
61 if (plot_default) {
62 channels <- c(grep(colnames(fcs), pattern="Forward scatter", ignore.case=TRUE),
63 grep(colnames(fcs), pattern="Side scatter", ignore.case=TRUE))
64 if (length(channels) == 0){
65 channels <- c(grep(colnames(fcs), pattern="FSC"),
66 grep(colnames(fcs), pattern="SSC"))
67 if (length(channels) > 2) {
68 #get first FSC and corresponding SSC
69 channels <- c(grep(colnames(fcs), pattern="FSC-A"),
70 grep(colnames(fcs), pattern="SSC-A"))
71 if (length(channels) == 0) {
72 channels <- c(grep(colnames(fcs), pattern="FSC-H"),
73 grep(colnames(fcs), pattern="SSC-H"))
74 if (length(channels) == 0) {
75 channels <- c(grep(colnames(fcs), pattern="FSC-W"),
76 grep(colnames(fcs), pattern="SSC-W"))
77 }
78 }
79 }
80 }
81 if (length(channels) == 0) {
82 warning('No forward/side scatter channels found, no plots will be generated.')
83 quit(save = "no", status = 10, runLast = FALSE)
84 }
85 }
86
87 nb_markers <- length(channels)
88
89 for (j in nb_markers) {
90 if (channels[j] > length(markers)){
91 warning('Please indicate markers between 1 and ', length(markers))
92 quit(save = "no", status = 10, runLast = FALSE)
93 }
94 }
95
96 plots <- list()
97 i <- 0
98 for (m in 1:(nb_markers - 1)) {
99 for (n in (m+1):nb_markers) {
100 x <- fcs[,channels[m]]
101 y <- fcs[,channels[n]]
102 df <- data.frame(x = x, y = y,
103 d = densCols(x, y, colramp = colorRampPalette(rev(rainbow(10, end = 4/6)))))
104 p <- ggplot(df) +
105 geom_point(aes(x, y, col = d), size = 0.2) +
106 scale_color_identity() +
107 theme_bw() +
108 labs(x = markers[channels[m]]) +
109 labs(y = markers[channels[n]])
110 i <- i + 1
111 plots[[i]] <- p
112 }
113 }
114 png(output, type="cairo", width=800, height=800)
115 multiplot(plotlist = plots, cols = 2)
116 dev.off()
117 if (flag_pdf){
118 pdf(pdf_out, useDingbats=FALSE, onefile=TRUE)
119 multiplot(plotlist = plots, cols = 2)
120 dev.off()
121 }
122 }
123
124 args <- commandArgs(trailingOnly = TRUE)
125 channels <- ""
126 flag_default <- FALSE
127 flag_pdf <- FALSE
128 pdf_output <- ""
129
130 if (args[3]=="None") {
131 flag_default <- TRUE
132 } else {
133 if (args[3] == "i.e.:1,3,4"){
134 flag_default <- TRUE
135 } else {
136 channels <- as.numeric(strsplit(args[3], ",")[[1]])
137 for (channel in channels){
138 if (is.na(channel)){
139 quit(save = "no", status = 11, runLast = FALSE)
140 }
141 }
142 if (length(channels) == 1){
143 warning('Please indicate more than one marker to plot.')
144 quit(save = "no", status = 10, runLast = FALSE)
145 }
146 }
147 }
148
149 if (args[5] == "TRUE"){
150 pdf_output <- args[6]
151 flag_pdf <- TRUE
152 }
153 generateGraphFromText(args[2], channels, args[4], flag_default, flag_pdf, pdf_output)