Mercurial > repos > azomics > ggcyto_1d_density_plots

comparison FCS1Dplotggcyto.R @ 0:b73fc4860906 draft default tip

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/ggcyto_1d_density_plots commit b32c86c02e138aa291c869b31351c4970300fbb4"
author azomics
date Mon, 22 Jun 2020 17:53:11 -0400
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-1:000000000000 0:b73fc4860906
1 #!/usr/bin/Rscript
2 # 1D Density Plot Module for Galaxy
3 # ggcyto
4 ######################################################################
5 # Copyright (c) 2016 Northrop Grumman.
6 # All rights reserved.
7 ######################################################################
8 #
9 # Version 1
10 # Cristel Thomas
11 #
12 #
13
14 library(ggcyto)
15
16 generate1Dplot <- function(input, output, flag_pdf=FALSE, trans_method="None",
17 factor="", log_w=0.5, log_t=262144, log_m=4.5) {
18 fcsfs <- read.flowSet(input, transformation=F)
19 h <- 800
20 w <- 1200
21 if ("colnames" %in% names(attributes(fcsfs)) && length(fcsfs@colnames)>12){
22 h <- 1200
23 w <- 1600
24 }
25 p <- autoplot(fcsfs[[1]])
26 if (trans_method == "arcsinh") {
27 p <- p + scale_x_flowCore_fasinh(a = 0, b = factor, c = 0) + geom_density(fill="steelblue", alpha=0.5)
28 } else if (trans_method == "logicle") {
29 p <- p + scale_x_logicle(w=log_w, t=log_t, m=log_m) + geom_density(fill="paleturquoise", alpha=0.5)
30 }
31
32 if (flag_pdf) {
33 pdf(output, useDingbats=FALSE, onefile=TRUE)
34 print({
35 p
36 })
37 dev.off()
38 } else {
39 png(output, type="cairo", height=h, width=w)
40 print({
41 p
42 })
43 dev.off()
44 }
45 }
46
47 checkFCS <- function(input_file, output_file, flag_pdf=FALSE, trans_met="None",
48 factor="", w=0.5, t=262144, m=4.5) {
49 isValid <- F
50 # Check file beginning matches FCS standard
51 tryCatch({
52 isValid <- isFCSfile(input_file)
53 }, error = function(ex) {
54 print (paste(" ! Error in isFCSfile", ex))
55 })
56
57 if (isValid) {
58 generate1Dplot(input_file, output_file, flag_pdf, trans_met,
59 factor, w, t, m)
60 } else {
61 print (paste(input_file, "does not meet FCS standard"))
62 }
63 }
64
65 args <- commandArgs(trailingOnly = TRUE)
66 flag_pdf <- FALSE
67 trans_method <- "None"
68 scaling_factor <- 1 / 150
69 w <- 0.5
70 t <- 262144
71 m <- 4.5
72
73 if (args[3] == "PDF"){
74 flag_pdf <- TRUE
75 }
76
77 if (args[4]!="None"){
78 trans_method <- args[4]
79 if (args[4] == "arcsinh"){
80 scaling_factor <- 1 / as.numeric(args[5])
81 } else if (args[4] == "logicle"){
82 w <- args[5]
83 t <- args[6]
84 m <- args[7]
85 }
86 }
87
88 checkFCS(args[1], args[2], flag_pdf, trans_method, scaling_factor, w, t, m)