Mercurial > repos > azomics > ggcyto_1d_density_plots

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