Mercurial > repos > iuc > raceid_trajectory
annotate scripts/trajectoryinspect.R @ 4:3e5bb16abb55 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
author | iuc |
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date | Mon, 12 Aug 2019 13:02:23 -0400 |
parents | ff7cd3c7c1df |
children | 72979cac22b2 |
rev | line source |
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0
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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1 #!/usr/bin/env R |
ff7cd3c7c1df
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" |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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3 |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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4 args = commandArgs(trailingOnly = T) |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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5 |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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6 if (length(args) != 1){ |
ff7cd3c7c1df
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)) |
ff7cd3c7c1df
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") |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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9 } |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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10 |
ff7cd3c7c1df
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))) |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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12 suppressWarnings(suppressPackageStartupMessages(require(FateID))) |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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13 source(args[1]) |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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14 |
ff7cd3c7c1df
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() |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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16 test$side = 3 |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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17 test$line = 2.5 |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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18 second <- test |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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19 second$cex = 0.5 |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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20 second$line = 2.5 |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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21 |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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22 do.trajectoryinspection.stemID <- function(ltr){ |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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23 makeBranchLink <- function(i,j,k){ |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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24 ingoing <- paste(sort(c(i,j)), collapse=".") |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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25 outgoing <- paste(sort(c(j,k)), collapse=".") |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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26 messed <- sort(c(ingoing,outgoing)) |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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27 return(list(messed[[1]], messed[[2]])) |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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28 } |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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29 |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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30 zzz <- do.call(getproj, c(ltr, trjsid.getproj)) |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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31 bra <- branchcells( |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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32 ltr, |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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33 do.call("makeBranchLink", as.list(trjsid.branchcells.ijk)) |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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34 ) |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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35 write.table( |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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36 head(bra$diffgenes$z, trjsid.numdiffgenes), |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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37 file=out.diffgenes) |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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38 |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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39 par(mfrow = c(2,2), cex=0.5) |
ff7cd3c7c1df
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(plotmap, c(bra$scl, final=FALSE, fr=FALSE))) |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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41 print(do.call(mtext, c("Initial Clusters (tSNE)", test))) |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
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42 print(do.call(plotmap, c(bra$scl, final=TRUE, fr=FALSE))) |
ff7cd3c7c1df
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(mtext, c("Final Clusters (tSNE)", test))) |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
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44 print(do.call(plotmap, c(bra$scl, final=FALSE, fr=TRUE))) |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
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45 print(do.call(mtext, c("Initial Clusters (F-R)", test))) |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
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46 print(do.call(plotmap, c(bra$scl, final=TRUE, fr=TRUE))) |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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47 print(do.call(mtext, c("Final Clusters (F-R)", test))) |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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48 } |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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49 |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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50 do.trajectoryinspection.fateID <- function(ltr){ |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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51 n <- do.call(cellsfromtree, c(ltr, trjfid.cellsfrom)) |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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52 x <- getfdata(ltr@sc) |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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53 |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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54 trjfid.filterset$x = x |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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55 trjfid.filterset$n = n$f |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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56 fs <- do.call(filterset, c(trjfid.filterset)) |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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57 trjfid.getsom$x = fs |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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58 s1d <- do.call(getsom, c(trjfid.getsom)) |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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59 trjfid.procsom$s1d = s1d |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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60 ps <- do.call(procsom, c(trjfid.procsom)) |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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61 |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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62 y <- ltr@sc@cpart[n$f] |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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63 fcol <- ltr@sc@fcol |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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64 |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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65 trjfid.plotheat$xpart = y |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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66 trjfid.plotheat$xcol = fcol |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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67 |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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68 ##Plot average z-score for all modules derived from the SOM: |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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69 trjfid.plotheat$x = ps$nodes.z |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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70 trjfid.plotheat$ypart = unique(ps$nodes) |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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71 print(do.call(plotheatmap, c(trjfid.plotheat))) |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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72 print(do.call(mtext, c("Average z-score for all modules derived from SOM", test))) |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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73 ##Plot z-score profile of each gene ordered by SOM modules: |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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74 trjfid.plotheat$x = ps$all.z |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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75 trjfid.plotheat$ypart = ps$nodes |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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76 print(do.call(plotheatmap, c(trjfid.plotheat))) |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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77 print(do.call(mtext, c("z-score profile of each gene ordered by SOM modules", test))) |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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78 ##Plot normalized expression profile of each gene ordered by SOM modules: |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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79 trjfid.plotheat$x = ps$all.e |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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80 trjfid.plotheat$ypart = ps$nodes |
ff7cd3c7c1df
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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81 print(do.call(plotheatmap, c(trjfid.plotheat))) |
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82 print(do.call(mtext, c("Normalized expression profile of each gene ordered by SOM modules", test))) |
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83 ##Plot binarized expression profile of each gene (z-score < -1, -1 < z-score < 1, z-score > 1): |
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84 trjfid.plotheat$x = ps$all.b |
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85 trjfid.plotheat$ypart = ps$nodes |
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86 print(do.call(plotheatmap, c(trjfid.plotheat))) |
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87 print(do.call(mtext, c("Binarized expression profile of each gene", test))) |
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88 ## This should be written out, and passed back into the tool |
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89 ## to perform sominspect |
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90 return(list(fs=fs,ps=ps,y=y,fcol=fcol,nf=n$f)) |
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91 } |
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92 |
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93 do.trajectoryinspection.fateID.sominspect <- function(domo){ |
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94 g <- trjfidsomi.use.genes |
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95 if (class(g) == "numeric"){ |
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96 g <- names(ps$nodes)[ps$nodes %in% g] |
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97 } |
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98 |
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99 typ = NULL |
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100 if (!is.null(trjfidsomi.use.types)){ |
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101 typ = sub(trjfidsomi.use.types,"", domo$nf) |
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102 } |
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103 |
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104 trjfidsomi$x = domo$fs |
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105 trjfidsomi$y = domo$y |
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106 trjfidsomi$g = g |
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107 trjfidsomi$n = domo$nf |
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108 trjfidsomi$col = domo$fcol |
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109 trjfidsomi$types = typ |
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110 |
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111 ## The average pseudo-temporal expression profile of this group |
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112 ## can be plotted by the function plotexpression: |
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113 par(mfrow = c(1,1)) |
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114 test$cex = 1 |
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115 second$line = 1.5 |
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116 if (trjfidsomi$name == "Title") trjfidsomi$name = "" |
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117 print(do.call(plotexpression, c(trjfidsomi))) |
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118 mess2 <- paste(c(trjfidsomi.use.genes), collapse=", ") |
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119 mess1 <- "Average pseudo-temporal expression profile" |
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120 print(do.call(mtext, c(mess1, test))) |
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121 print(do.call(mtext, c(mess2, second))) |
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122 } |
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123 |
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124 ltr <- in.rdat |
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125 |
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126 pdf(out.pdf) |
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127 if (perform.stemID) do.trajectoryinspection.stemID(ltr) |
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128 if (perform.fateID) { |
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129 domo <- do.trajectoryinspection.fateID(ltr) |
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130 if (perform.fateID.sominspect) { |
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131 do.trajectoryinspection.fateID.sominspect(domo) |
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132 } |
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133 } |
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134 dev.off() |