Mercurial > repos > azomics > metacyto_histogram

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"planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
author azomics
date Thu, 29 Jul 2021 22:15:11 +0000
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f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
azomics
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1 #!/usr/bin/env Rscript
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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2 ######################################################################
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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3 # Copyright (c) 2018 Northrop Grumman.
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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4 # All rights reserved.
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
azomics
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5 ######################################################################
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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6 #
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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7 # Version 1 - January 2018
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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8 # Author: Cristel Thomas
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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9 #
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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10 #
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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11
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
azomics
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12 library(flowCore)
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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13 library(MetaCyto)
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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14
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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15 check_cluster_def <- function(cl_def) {
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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16 if (cl_def == "" || cl_def == "None") {
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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17 quit(save = "no", status = 12, runLast = FALSE)
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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18 } else {
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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19 tmp <- gsub(" ", "", cl_def, fixed = TRUE)
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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20 clean_def <- gsub(",", "|", tmp, fixed = TRUE)
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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21 return(clean_def)
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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22 }
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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23 }
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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24
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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25 generate_plots <- function(fpath = "", fname = "", gates = vector(), outdir = "", uc = "",
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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26 flag_pdf = F) {
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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27 dir.create(outdir)
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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28 ff <- read.FCS(fpath, truncate_max_range = F)
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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29 markers <- markerFinder(ff)
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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30 colnames(ff@exprs) <- markers
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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31
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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32 sc <- searchCluster(fcsFrame = ff, clusterLabel = gates)
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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33
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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34 if (length(gates) == length(sc$clusterList)) {
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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35 sink(uc)
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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36 cat("All provided cluster definition were used.")
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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37 sink()
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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38 } else {
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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39 unused_cluster <- setdiff(gates, names(sc$clusterList))
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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40 write.table(unused_cluster, uc, quote = F, row.names = F, col.names = F)
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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41 }
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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42
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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43 groupname <- unlist(strsplit(fname, ".fcs"))[[1]]
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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44 extension <- if (flag_pdf) "plot.pdf" else "plot.png"
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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45 for (i in seq_len(length(sc$clusterList))) {
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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46 gate <- gsub("|", "", names(sc$clusterList[i]), fixed = T)
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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47 plotname <- paste(c(groupname, gate, extension), collapse = "_")
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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48 outplot <- file.path(outdir, plotname)
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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49 if (flag_pdf) {
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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50 pdf(outplot, useDingbats = F, onefile = T)
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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51 par(mfrow = c(2, 2))
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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52 for (j in seq_len(length(markers))) {
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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53 if (markers[[j]] != "SAMPLE_ID" && markers[[j]] != "TIME") {
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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54 plot_title <- paste0(markers[[j]], ", cluster definition:\n", gate)
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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55 x_all <- ff@exprs[, markers[[j]]]
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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56 b <- seq(min(x_all), max(x_all), ((max(x_all) - min(x_all)) / 100))
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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57 subset <- ff@exprs[sc$clusterList[[i]], markers[[j]]]
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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58 hist(x_all, col = rgb(0, 0, 0), xlab = markers[[j]], breaks = b, freq = T,
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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59 border = F, main = plot_title)
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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60 hist(subset, add = T, breaks = b, col = rgb(1, 0, 0), freq = T, border = F)
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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61 if (markers[[j]] %in% names(sc$cutoff)) {
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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62 abline(v = sc$cutoff[markers[[j]]])
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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63 }
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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64 }
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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65 }
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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66 dev.off()
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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67 } else {
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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68 markers_ct <- length(markers) - length(grep(x = markers, pattern = "SAMPLE_ID|TIME"))
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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69 nb_rows <- ceiling(markers_ct / 2)
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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70 h <- nb_rows * 400
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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71 png(outplot, type = "cairo", height = h, width = 800)
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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72 par(mfrow = c(nb_rows, 2))
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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73 for (j in seq_len(length(markers))) {
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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74 if (markers[[j]] != "SAMPLE_ID" && markers[[j]] != "TIME") {
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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75 plot_title <- paste0(markers[[j]], ", cluster definition:\n", gate)
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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76 x_all <- ff@exprs[, markers[[j]]]
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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77 b <- seq(min(x_all), max(x_all), ((max(x_all) - min(x_all)) / 100))
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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78 subset <- ff@exprs[sc$clusterList[[i]], markers[[j]]]
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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79 hist(x_all, col = rgb(0, 0, 0), xlab = markers[[j]], breaks = b, freq = T,
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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80 border = F, main = plot_title)
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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81 hist(subset, add = T, breaks = b, col = rgb(1, 0, 0), freq = T, border = F)
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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82 if (markers[[j]] %in% names(sc$cutoff)) {
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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83 abline(v = sc$cutoff[markers[[j]]])
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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84 }
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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85 }
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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86 }
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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87 dev.off()
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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88 }
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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89 }
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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90 }
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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91
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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92 check_fcs_file <- function(inputf="", inputn="", clusters=vector(),
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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93 output_dir = "", unused = "", flag = F) {
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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94 is_valid <- FALSE
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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95 tryCatch({
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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96 is_valid <- isFCSfile(inputf)
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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97 }, error = function(ex) {
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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98 print(paste("Input file is not a valid FCS file.", ex))
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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99 })
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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100 if (is_valid) {
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101 generate_plots(inputf, inputn, clusters, output_dir, unused, flag)
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102 } else {
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103 quit(save = "no", status = 12, runLast = FALSE)
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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104 }
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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105 }
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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106
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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107 ################################################################################
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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108 ################################################################################
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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109 args <- commandArgs(trailingOnly = TRUE)
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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110
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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111 gates <- vector()
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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112 if (args[6] == "F") {
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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113 ## obvs deal with it if file
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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114 cluster_file <- read.table(args[7], header = F, colClasses = "character")
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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115 gates <- unlist(cluster_file)
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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116 } else {
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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117 cl_df <- args[7:length(args)]
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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118 gates <- sapply(cl_df, check_cluster_def)
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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119 }
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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120
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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121 flag_pdf <- if (args[5] == "PDF") TRUE else FALSE
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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122 gate_list <- toupper(gates)
f5526d97056c "planemo upload for repository https://github.com/AstraZeneca-Omics/immport-galaxy-tools/tree/master/flowtools/metacyto_histogram commit cb978232e32b64f7b0ff3c1852e708361045d268"
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123 check_fcs_file(args[1], args[2], gate_list, args[3], args[4], flag_pdf)