Mercurial > repos > immport-devteam > flowtext_scatterplot

comparison getDensityPlots_text.R @ 1:754d511df1a3 draft default tip

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowtext_scatterplot commit 2944aa6b74efcdb8d5cbf31abf27b352dcad9ac9"
author azomics
date Tue, 14 Jul 2020 09:40:13 -0400
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0:cc2266d3e611 1:754d511df1a3
1 #!/usr/bin/env Rscript
2 # Density Plot Module for Galaxy
3 # ggplot2
4 ######################################################################
5 # Copyright (c) 2016 Northrop Grumman.
6 # All rights reserved.
7 ######################################################################
8 #
9 # Version 1
10 # Cristel Thomas
11 #
12 #
13
14 library(ggplot2)
15 library(grid)
16 library(KernSmooth)
17 # Multiple plot function
18 # from http://www.cookbook-r.com/Graphs/Multiple_graphs_on_one_page_%28ggplot2%29/
19 # ggplot objects can be passed in ..., or to plotlist (as a list of ggplot objects)
20 # - cols: Number of columns in layout
21 # - layout: A matrix specifying the layout. If present, 'cols' is ignored.
22 #
23 # If the layout is something like matrix(c(1,2,3,3), nrow=2, byrow=TRUE),
24 # then plot 1 will go in the upper left, 2 will go in the upper right, and
25 # 3 will go all the way across the bottom.
26 #
27 multiplot <- function(..., plotlist=NULL, file, cols=1, layout=NULL) {
28 # Make a list from the ... arguments and plotlist
29 plots <- c(list(...), plotlist)
30 numPlots = length(plots)
31
32 # If layout is NULL, then use 'cols' to determine layout
33 if (is.null(layout)) {
34 # Make the panel
35 # ncol: Number of columns of plots
36 # nrow: Number of rows needed, calculated from # of cols
37 layout <- matrix(seq(1, cols * ceiling(numPlots/cols)),
38 ncol = cols, nrow = ceiling(numPlots/cols))
39 }
40
41 if (numPlots==1) {
42 print(plots[[1]])
43 } else {
44 # Set up the page
45 grid.newpage()
46 pushViewport(viewport(layout = grid.layout(nrow(layout), ncol(layout))))
47
48 # Make each plot, in the correct location
49 for (i in 1:numPlots) {
50 # Get the i,j matrix positions of the regions that contain this subplot
51 matchidx <- as.data.frame(which(layout == i, arr.ind = TRUE))
52 print(plots[[i]], vp = viewport(layout.pos.row = matchidx$row,
53 layout.pos.col = matchidx$col))
54 }
55 }
56 }
57
58 generateGraphFromText <- function(input, channels, output, plot_default=TRUE,
59 flag_pdf=FALSE) {
60 fcs <- read.table(input, header = TRUE, sep = "\t", check.names = FALSE)
61 ## marker names
62 markers <- colnames(fcs)
63
64 if (plot_default) {
65 channels <- c(grep(colnames(fcs), pattern="Forward scatter", ignore.case=TRUE),
66 grep(colnames(fcs), pattern="Side scatter", ignore.case=TRUE))
67 if (length(channels) == 0){
68 channels <- c(grep(colnames(fcs), pattern="FSC"),
69 grep(colnames(fcs), pattern="SSC"))
70 if (length(channels) > 2) {
71 #get first FSC and corresponding SSC
72 channels <- c(grep(colnames(fcs), pattern="FSC-A"),
73 grep(colnames(fcs), pattern="SSC-A"))
74 if (length(channels) == 0) {
75 channels <- c(grep(colnames(fcs), pattern="FSC-H"),
76 grep(colnames(fcs), pattern="SSC-H"))
77 if (length(channels) == 0) {
78 channels <- c(grep(colnames(fcs), pattern="FSC-W"),
79 grep(colnames(fcs), pattern="SSC-W"))
80 }
81 }
82 }
83 }
84 if (length(channels) == 0) {
85 warning('No forward/side scatter channels found, no plots will be generated.')
86 quit(save = "no", status = 10, runLast = FALSE)
87 }
88 }
89
90 nb_markers <- length(channels)
91 if (nb_markers == 1) {
92 warning('There is only one marker selected to plot.')
93 quit(save = "no", status = 12, runLast = FALSE)
94 }
95 for (j in nb_markers) {
96 if (channels[j] > length(markers)){
97 warning('Please indicate markers between 1 and ', length(markers))
98 quit(save = "no", status = 10, runLast = FALSE)
99 }
100 }
101
102 plots <- list()
103 i <- 0
104 for (m in 1:(nb_markers - 1)) {
105 for (n in (m+1):nb_markers) {
106 x <- fcs[,channels[m]]
107 y <- fcs[,channels[n]]
108 df <- data.frame(x = x, y = y,
109 d = densCols(x, y, colramp = colorRampPalette(rev(rainbow(10, end = 4/6)))))
110 p <- ggplot(df) +
111 geom_point(aes(x, y, col = d), size = 0.2) +
112 scale_color_identity() +
113 theme_bw() +
114 labs(x = markers[channels[m]]) +
115 labs(y = markers[channels[n]])
116 i <- i + 1
117 plots[[i]] <- p
118 }
119 }
120 nb_rows <- ceiling(((nb_markers-1)*nb_markers)/4)
121 h <- 400 * nb_rows
122 hp <- 10 * (nb_rows/2)
123
124 if (flag_pdf){
125 pdf(output, height=hp, width=10, useDingbats=FALSE, onefile=TRUE)
126 multiplot(plotlist = plots, cols = 2)
127 dev.off()
128 } else {
129 png(output, type="cairo", width=800, height=h)
130 multiplot(plotlist = plots, cols = 2)
131 dev.off()
132 }
133 }
134
135 args <- commandArgs(trailingOnly = TRUE)
136 channels <- list()
137 flag_default <- FALSE
138 flag_pdf <- FALSE
139
140 if (args[2]=="None" || args[2]== "" || args[2] == "i.e.:1,3,4") {
141 flag_default <- TRUE
142 } else {
143 channels <- as.numeric(strsplit(args[2], ",")[[1]])
144 for (channel in channels){
145 if (is.na(channel)){
146 quit(save = "no", status = 11, runLast = FALSE)
147 }
148 }
149 if (length(channels) == 1){
150 warning('Please indicate more than one marker to plot.')
151 quit(save = "no", status = 10, runLast = FALSE)
152 }
153 }
154
155 if (args[4] == "PDF"){
156 flag_pdf <- TRUE
157 }
158 generateGraphFromText(args[1], channels, args[3], flag_default, flag_pdf)