Mercurial > repos > iuc > raceid_inspectclusters
annotate scripts/clusterinspect.R @ 0:9fec5dd8fbb9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
author | iuc |
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date | Thu, 22 Nov 2018 04:45:41 -0500 |
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children | 20f522154663 |
rev | line source |
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0
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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1 #!/usr/bin/env R |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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2 VERSION = "0.2" |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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3 |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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4 args = commandArgs(trailingOnly = T) |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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5 |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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changeset
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6 if (length(args) != 1){ |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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7 message(paste("VERSION:", VERSION)) |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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8 stop("Please provide the config file") |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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9 } |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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10 |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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11 suppressWarnings(suppressPackageStartupMessages(require(RaceID))) |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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12 source(args[1]) |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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13 |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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14 ## layout |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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15 test <- list() |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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16 test$side = 3 |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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17 test$line = 3 |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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18 |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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19 do.plotting <- function(sc){ |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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20 print(plotmap(sc, final = FALSE, fr = FALSE)) |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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21 print(do.call(mtext, c("Initial Clustering tSNE", test))) |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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22 print(plotmap(sc, final = TRUE, fr = FALSE)) |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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23 print(do.call(mtext, c("Final Clustering tSNE", test))) |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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24 print(plotmap(sc, final = FALSE, fr = TRUE)) |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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25 print(do.call(mtext, c("Initial Clustering Fruchterman-Reingold", test))) |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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changeset
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26 print(plotmap(sc, final = TRUE, fr = TRUE)) |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
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27 print(do.call(mtext, c("Final Clustering Fruchterman-Reingold", test))) |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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28 } |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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29 |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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30 |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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31 do.inspect.symbolmap <- function(sc){ |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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32 if (!is.null(plotsym.use.typeremoveregex)){ |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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33 plotsym$types = sub(plotsym.use.typeremoveregex, "", colnames(sc@ndata)) |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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34 |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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35 if (!is.null(plotsym.use.typeremoveregex.subselect)){ |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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36 plotsym$subset = plotsym$types[grep(plotsym.use.typeremoveregex.subselect, plotsym$types)] |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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37 } |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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38 } |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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39 plotsym$fr = FALSE |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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40 print(do.call(plotsymbolsmap, c(sc, plotsym))) |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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41 print(do.call(mtext, c("Symbols tSNE", test))) |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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42 plotsym$fr = TRUE |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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43 print(do.call(plotsymbolsmap, c(sc, plotsym))) |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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44 print(do.call(mtext, c("Symbols FR", test))) |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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45 } |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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46 |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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47 do.inspect.diffgene <- function(sc){ |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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48 |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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49 getSubNames <- function(lob, sc){ |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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50 use.names <- NULL |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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51 if (!is.null(lob$manual)){ |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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52 use.names <- lob$manual |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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53 } |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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54 else if (!is.null(lob$regex)){ |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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55 nm <- colnames(sc@ndata) |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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56 use.names <- nm[grep(lob$regex, nm)] |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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57 } |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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58 else if (!is.null(lob$cln)){ |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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59 use.names <- names(sc@cpart)[sc@cpart %in% lob$cln] |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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60 } |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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61 if (is.null(use.names)){ |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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62 stop("A or B names not given!") |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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63 } |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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64 return(use.names) |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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65 } |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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66 |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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67 A <- getSubNames(gfdat.A.use, sc) |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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68 B <- getSubNames(gfdat.B.use, sc) |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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69 |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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70 fdat <- getfdata(sc, n=c(A,B)) |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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71 dexp <- diffexpnb(fdat, A=A, B=B) |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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72 ## options for diffexpnb are mostly about DESeq, ignore |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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73 plotdiffg$x = dexp |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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74 print(do.call(plotdiffgenesnb, c(plotdiffg))) |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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75 print(do.call(mtext, c("Diff Genes", test))) |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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76 } |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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77 |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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78 |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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79 do.inspect.genesofinterest <- function(sc){ |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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80 if (is.null(plotexp$n)){ ## No title, and one gene? Use gene name |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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81 if (length(plotexp$g) == 1){ |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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82 plotexp$n <- plotexp$g |
9fec5dd8fbb9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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83 } else { |
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84 plotexp$n <- paste(plotexp$g, collapse=", ") |
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85 } |
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86 } |
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87 |
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88 title <- paste(":", plotexp$n) |
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89 plotexp$n <- "" |
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90 |
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91 plotexp$logsc=FALSE; plotexp$fr = FALSE |
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92 print(do.call(plotexpmap, c(sc, plotexp))) |
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93 print(do.call(mtext, c(paste("tSNE", title), test))) |
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94 |
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95 plotexp$logsc=TRUE; plotexp$fr = FALSE |
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96 print(do.call(plotexpmap, c(sc, plotexp))) |
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97 print(do.call(mtext, c(paste("tSNE (Log)", title), test))) |
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98 |
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99 plotexp$logsc=FALSE; plotexp$fr = TRUE |
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100 print(do.call(plotexpmap, c(sc, plotexp))) |
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101 print(do.call(mtext, c(paste("FR", title), test))) |
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102 |
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103 plotexp$logsc=TRUE; plotexp$fr = TRUE |
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104 print(do.call(plotexpmap, c(sc, plotexp))) |
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105 print(do.call(mtext, c(paste("FR (Log)", title), test))) |
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106 |
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107 if (!is.null(plotmarkg$samples)){ |
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108 reg <- plotmarkg$samples |
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109 plotmarkg$samples <- sub("(\\_\\d+)$","", colnames(sc@ndata)) |
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110 } |
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111 print(do.call(plotmarkergenes, c(sc, plotmarkg))) |
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112 } |
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113 |
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114 sc <- in.rdat |
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115 |
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116 pdf(out.pdf) |
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117 if (perform.plotting) do.plotting(sc) |
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118 if (perform.symbolmap) do.inspect.symbolmap(sc) |
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119 if (perform.genesofinterest) do.inspect.genesofinterest(sc) |
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120 if (perform.diffgene) do.inspect.diffgene(sc) |
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121 dev.off() |