Mercurial > repos > azomics > flowviz_density_plots

annotate FCSflowViz.R @ 0:23c0af6be9a7 draft default tip

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
author azomics
date Mon, 22 Jun 2020 20:48:47 -0400
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23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
parents:
diff changeset
1 #!/usr/bin/Rscript
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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diff changeset
2 # Stacked 1D Density Plot Module for Galaxy
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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diff changeset
3 # flowviz
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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4 ######################################################################
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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5 # Copyright (c) 2016 Northrop Grumman.
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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6 # All rights reserved.
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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7 ######################################################################
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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8 #
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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9 # Version 1
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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10 # Cristel Thomas
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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11 #
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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12 #
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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13
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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14 library(flowViz)
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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15 library(methods)
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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16
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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17 generateStackedPlots <- function(fs, chans=list(), output="", flag_pdf=FALSE) {
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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diff changeset
18 h <- 800
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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19 w <- 1200
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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20 if (length(fs@colnames)>8){
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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21 h <- 1200
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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22 w <- 1600
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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23 }
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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24 channels_to_plot <- fs@colnames
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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25 if (length(chans) > 0){
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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26 channels_to_plot <- fs@colnames[chans]
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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27 }
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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28
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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29 if (flag_pdf) {
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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30 pdf(output, useDingbats=FALSE, onefile=TRUE)
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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31 print({
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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32 densityplot(~., fs, channels = channels_to_plot)
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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33 })
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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34 dev.off()
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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diff changeset
35 } else {
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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36 png(output, type="cairo", height=h, width=w)
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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37 print({
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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38 densityplot(~., fs, channels = channels_to_plot)
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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39 })
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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diff changeset
40 dev.off()
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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41 }
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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42 }
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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43
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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44 checkFlowSet <- function(fcsfiles, newnames, channels=list(), out_file ="",
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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45 flag_pdf=FALSE) {
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
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46
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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47 isValid <- F
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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48 markerCheck <- T
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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49
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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50 for (i in 1:length(fcsfiles)){
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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51 is_file_valid <- F
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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52 tryCatch({
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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53 fcs <- read.FCS(fcsfiles[i], transformation=FALSE)
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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54 is_file_valid <- T
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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55 }, error = function(ex) {
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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56 print(paste(ex))
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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57 })
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
parents:
diff changeset
58 if (i == 1) {
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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59 m1 <- as.vector(pData(parameters(fcs))$desc)
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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60 } else {
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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61 m2 <- as.vector(pData(parameters(fcs))$desc)
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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62 if (is.na(all(m1==m2))) {
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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63 mm1 <- is.na(m1)
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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64 mm2 <- is.na(m2)
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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65 if (all(mm1==mm2)){
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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66 if (!all(m1==m2, na.rm=TRUE)){
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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67 markerCheck <- F
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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68 }
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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69 } else {
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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70 markerCheck <- F
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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71 }
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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72 } else if (!all(m1==m2)) {
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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73 markerCheck <- F
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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74 }
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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75 }
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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76 }
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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77 if (markerCheck) {
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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78 isValid <- T
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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79 } else {
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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80 quit(save = "no", status = 12, runLast = FALSE)
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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81 }
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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82
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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83 if (isValid) {
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
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84 fs <- read.flowSet(files=fcsfiles, transformation=FALSE)
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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85 fs@phenoData@data$name <- newnames
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
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86 generateStackedPlots(fs, channels, out_file, flag_pdf)
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
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87 } else {
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
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88 quit(save = "no", status = 12, runLast = FALSE)
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
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89 }
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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90 }
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
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91
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
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92 args <- commandArgs(trailingOnly = TRUE)
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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93 channels <- list()
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
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94 flag_pdf <- FALSE
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
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95
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
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96 if (args[1]=="None") {
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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97 flag_default <- TRUE
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
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98 } else {
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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99 if (args[1] == "i.e.:1,3,4"){
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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100 flag_default <- TRUE
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
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101 } else {
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
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102 channels <- as.numeric(strsplit(args[1], ",")[[1]])
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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103 for (channel in channels){
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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104 if (is.na(channel)){
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
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105 quit(save = "no", status = 11, runLast = FALSE)
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
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106 }
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
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107 }
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
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108 }
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
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109 }
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
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110
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
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111 if (args[3] == "PDF"){
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
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112 flag_pdf <- TRUE
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
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113 }
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
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114
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
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115 nb_files <- (length(args) - 3) / 2
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
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116 fcsfiles <- character(nb_files)
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
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117 newnames <- character(nb_files)
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
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118 j <- 1
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
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119 ## get files and file names
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
azomics
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120 for (i in 4:length(args)) {
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
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121 if (!i%%2){
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
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122 fcsfiles[[j]] <- args[i]
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
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123 newnames[[j]] <- args[i+1]
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
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124 j <- j + 1
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
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125 }
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
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126 }
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
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127
23c0af6be9a7 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowviz_density_plots commit 8645b278253fe79de4a23fd3e54e397bca2a9919"
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128 checkFlowSet(fcsfiles, newnames, channels, args[2], flag_pdf)