Mercurial > repos > azomics > flowsom_compare
annotate FlowSOMCompare.R @ 0:bd35f3b66a1e draft
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
author | azomics |
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date | Mon, 22 Jun 2020 17:54:03 -0400 |
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children | 33b8673272cf |
rev | line source |
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0
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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1 #!/usr/bin/Rscript |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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2 # Module for Galaxy |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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3 # Compares groups of FCS to FlowSOM reference tree |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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4 # with FlowSOM |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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5 ###################################################################### |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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6 # Copyright (c) 2017 Northrop Grumman. |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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7 # All rights reserved. |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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8 ###################################################################### |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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9 # |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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10 # Version 1 |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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11 # Cristel Thomas |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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12 # |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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13 # |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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14 library(FlowSOM) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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15 library(flowCore) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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16 |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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17 checkFiles <- function(groups){ |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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18 all_files <- unlist(groups) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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19 all_unique <- unique(all_files) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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20 if (length(all_unique) != length(all_files)) { |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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21 quit(save = "no", status = 14, runLast = FALSE) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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22 } |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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23 } |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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24 |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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25 compareLists <- function(m1, m2){ |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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26 listCheck <- T |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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27 if (is.na(all(m1==m2))) { |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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28 mm1 <- is.na(m1) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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29 mm2 <- is.na(m2) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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30 if (all(mm1==mm2)){ |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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31 if (!all(m1==m2, na.rm=TRUE)){ |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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32 listCheck <- F |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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33 } |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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34 } else { |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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35 listCheck <- F |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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36 } |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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37 } else if (!all(m1==m2)) { |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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38 listCheck <- F |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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39 } |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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40 return(listCheck) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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41 } |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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42 |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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43 prettyMarkerNames <- function(flowFrame){ |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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44 n <- flowFrame@parameters@data[, "name"] |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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45 d <- flowFrame@parameters@data[, "desc"] |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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46 d[is.na(d)] <- n[is.na(d)] |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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47 prettyNames <- list() |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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48 if(any(grepl("#",d))){ |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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49 # Support for hashtag notation: |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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50 # antibody#fluorochrome -> antibody (fluorochrome) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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51 prettyNames <- gsub("#(.*)$"," (\\1)",d) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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52 } else { |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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53 prettyNames <- paste(d, " <", n, ">", sep="") |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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54 } |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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55 return(prettyNames) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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56 } |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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57 |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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58 compareToTree <- function(fst, wilc_thresh=0.05, output="", plot="", stats, |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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59 comp_groups, filenames) { |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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60 groupRes <- CountGroups(fst, groups=comp_groups, plot=FALSE) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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61 pdf(plot, useDingbats=FALSE, onefile=TRUE) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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62 tresh <- wilc_thresh |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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63 pg <- PlotGroups(fst, groupRes, p_tresh=tresh) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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64 dev.off() |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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65 |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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66 nb_nodes <- length(pg[[1]]) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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67 nb_comp <- length(pg) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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68 m <- matrix(0, nrow=nb_nodes, ncol=nb_comp+1) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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69 s <- seq_len(nb_nodes) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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70 m[,1]<- as.character(s) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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71 for (i in 1:nb_comp){ |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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72 m[s,i+1]<- as.character(pg[[i]]) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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73 } |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
diff
changeset
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74 groupnames <- attr(comp_groups,"names") |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
diff
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|
75 out_colnames <- paste(groupnames, collapse="-") |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
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|
76 colnames(m) <- c("Node",out_colnames) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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77 write.table(m, file=output, quote=F, row.names=F, col.names=T, sep='\t', |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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78 append=F) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
diff
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|
79 |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
diff
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80 ## get filenames |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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81 filepaths <- unlist(comp_groups) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
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82 fnames <- unlist(filenames) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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83 nb_files <- length(filepaths) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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84 comp_files <- list() |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
diff
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85 for (i in 1:length(filepaths)){ |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
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86 comp_files[[filepaths[[i]]]] <- fnames[[i]] |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
diff
changeset
|
87 } |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
diff
changeset
|
88 |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
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|
89 group_list <- list() |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
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90 for (grp in attr(comp_groups, "names")) { |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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diff
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91 for (f in comp_groups[[grp]]){ |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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92 group_list[[f]] <- grp |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
diff
changeset
|
93 } |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
diff
changeset
|
94 } |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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95 out_stats <- attr(stats, "names") |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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changeset
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96 if ("counts" %in% out_stats){ |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
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changeset
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97 gp_counts <- as.matrix(groupRes$counts) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
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98 tpc <- matrix("", nrow=nb_files, ncol=2) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
diff
changeset
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99 tpc[,1] <- as.character(lapply(rownames(gp_counts), function(x) comp_files[[x]])) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
diff
changeset
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100 tpc[,2] <- as.character(lapply(rownames(gp_counts), function(x) group_list[[x]])) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
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changeset
|
101 gp_counts <- cbind(tpc, gp_counts) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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102 colnames(gp_counts)[[1]] <- "Filename" |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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103 colnames(gp_counts)[[2]] <- "Group" |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
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changeset
|
104 t_gp_counts <- t(gp_counts) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
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changeset
|
105 write.table(t_gp_counts, file=stats[["counts"]], quote=F, row.names=T, col.names=F, sep='\t', |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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106 append=F) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
diff
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|
107 } |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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|
108 if ("pctgs" %in% out_stats){ |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
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|
109 gp_prop <- as.matrix(groupRes$pctgs) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
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|
110 tpp <- matrix("", nrow=nb_files, ncol=2) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
diff
changeset
|
111 tpp[,1] <- as.character(lapply(rownames(gp_prop), function(x) comp_files[[x]])) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
diff
changeset
|
112 tpp[,2] <- as.character(lapply(rownames(gp_prop), function(x) group_list[[x]])) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
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|
113 gp_prop <- cbind(tpp, gp_prop) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
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|
114 colnames(gp_prop)[[1]] <- "Filename" |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
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changeset
|
115 colnames(gp_prop)[[2]] <- "Group" |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
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|
116 t_gp_prop <- t(gp_prop) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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|
117 write.table(t_gp_prop, file=stats[["pctgs"]], quote=F, row.names=T, col.names=F, sep='\t', |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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118 append=F) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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diff
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|
119 } |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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|
120 if ("means" %in% out_stats){ |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
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121 gp_mean <- as.matrix(groupRes$means) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
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122 t_gp_mean <- t(gp_mean) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
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|
123 tpm <- matrix(0, nrow=nb_nodes, ncol=1) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
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|
124 tpm[,1] <- seq_len(nb_nodes) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
diff
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|
125 t_gp_mean <- cbind(tpm, t_gp_mean) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
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|
126 colnames(t_gp_mean)[[1]] <- "Nodes" |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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127 write.table(t_gp_mean, file=stats[["means"]], quote=F, row.names=F, col.names=T, sep='\t', |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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128 append=F) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
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|
129 } |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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|
130 if ("medians" %in% out_stats){ |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
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|
131 gp_med <- as.matrix(groupRes$medians) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
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|
132 t_gp_med <- t(gp_med) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
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|
133 tpd <- matrix(0, nrow=nb_nodes, ncol=1) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
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changeset
|
134 tpd[,1] <- seq_len(nb_nodes) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
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|
135 t_gp_med <- cbind(tpd, t_gp_med) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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changeset
|
136 colnames(t_gp_med)[[1]] <- "Nodes" |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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changeset
|
137 write.table(t_gp_med, file=stats[["medians"]], quote=F, row.names=F, col.names=T, sep='\t', |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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diff
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|
138 append=F) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
diff
changeset
|
139 } |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
diff
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|
140 } |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
diff
changeset
|
141 |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
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|
142 checkFCS <- function(tree, output="", plot="", thresh = 0.05, stats, groups, |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
diff
changeset
|
143 filenames) { |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
diff
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144 |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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145 fcsfiles <- unlist(groups) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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146 tree_valid <- F |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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147 markerCheck <- T |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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148 tryCatch({ |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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149 fsomtree <- readRDS(tree) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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150 tree_valid <- T |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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151 }, error = function(ex) { |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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152 print(paste(ex)) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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153 }) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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154 |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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155 fst <- if (length(fsomtree)==2) fsomtree[[1]] else fsomtree |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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156 |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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157 if (tree_valid){ |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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158 tree_markers <- as.vector(fst$prettyColnames) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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159 tree_channels <- as.vector(colnames(fst$data)) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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160 if (length(tree_markers) < 1){ |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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161 quit(save = "no", status = 11, runLast = FALSE) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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162 } |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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163 } else { |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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164 quit(save = "no", status = 11, runLast = FALSE) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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165 } |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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166 |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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167 for (i in 1:length(fcsfiles)){ |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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168 is_file_valid <- F |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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169 tryCatch({ |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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170 fcs <- read.FCS(fcsfiles[i], transformation=FALSE) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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171 is_file_valid <- T |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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172 }, error = function(ex) { |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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173 print(paste(ex)) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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174 }) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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175 if (i == 1) { |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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176 m1 <- as.vector(pData(parameters(fcs))$desc) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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177 c1 <- colnames(fcs) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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178 # compare to tree markers |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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179 pm <- prettyMarkerNames(fcs) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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180 if (!all(tree_markers %in% pm)){ |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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181 quit(save = "no", status = 13, runLast = FALSE) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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182 } |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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183 } else { |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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184 m2 <- as.vector(pData(parameters(fcs))$desc) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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185 c2 <- colnames(fcs) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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186 markerCheck <- compareLists(m1,m2) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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187 markerChannel <- compareLists(c1,c2) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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188 } |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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189 } |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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190 if (markerCheck && markerChannel) { |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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191 compareToTree(fst, thresh, output, plot, stats, groups, filenames) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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192 } else { |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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193 quit(save = "no", status = 12, runLast = FALSE) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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194 } |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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195 } |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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196 |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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197 args <- commandArgs(trailingOnly = TRUE) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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198 |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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199 first_g1 <- 5 |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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200 tot_args <- length(args) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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201 g <- list() |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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202 tmplist <- c("counts", "means", "medians", "pctgs") |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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203 |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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204 for (i in 5:13){ |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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205 if (args[i] %in% tmplist){ |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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206 first_g1 <- first_g1 + 2 |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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207 g[[args[i]]] <- args[i+1] |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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208 } |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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209 } |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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210 |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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|
211 tmpargs <- paste(args[first_g1:tot_args], collapse="=%=") |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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212 tmpgroups <- strsplit(tmpargs, "=%=DONE=%=") |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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213 |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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214 groups <- list() |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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215 filenames <- list() |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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|
216 for (gps in tmpgroups[[1]]) { |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
parents:
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|
217 tmpgroup <- strsplit(gps, "=%=") |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
azomics
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|
218 nb_files <- (length(tmpgroup[[1]]) - 1 ) /2 |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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219 tmplist <- character(nb_files) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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220 tmpnames <- character(nb_files) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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221 j <- 1 |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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222 for (i in 2:length(tmpgroup[[1]])){ |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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223 if (!i%%2){ |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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224 tmplist[[j]] <- tmpgroup[[1]][i] |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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225 tmpnames[[j]]<- tmpgroup[[1]][i+1] |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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226 j <- j + 1 |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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227 } |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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228 } |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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229 groups[[tmpgroup[[1]][1]]] <- tmplist |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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230 filenames[[tmpgroup[[1]][1]]] <- tmpnames |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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231 } |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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232 |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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233 checkFiles(groups) |
bd35f3b66a1e
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowsom_compare commit a1755b91905a2a95ebb0d6dd4a2b3d42c7e19f05"
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234 checkFCS(args[1], args[2], args[3], args[4], g, groups, filenames) |