Mercurial > repos > iuc > raceid_clustering

annotate scripts/trajectoryinspect.R @ 8:f911a64454fb draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 455bad7eca54164f95755174904842907846bb42"
author iuc
date Mon, 20 Dec 2021 10:12:47 +0000
parents a4b734cd253b
children 0bff0ee0683a
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4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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1 #!/usr/bin/env R
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2 VERSION <- "0.2" # nolint
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4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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4 args <- commandArgs(trailingOnly = T)
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4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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6 if (length(args) != 1) {
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4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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7 message(paste("VERSION:", VERSION))
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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8 stop("Please provide the config file")
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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9 }
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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11 suppressWarnings(suppressPackageStartupMessages(require(RaceID)))
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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12 suppressWarnings(suppressPackageStartupMessages(require(FateID)))
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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13 source(args[1])
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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15 test <- list()
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16 test$side <- 3
a4b734cd253b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
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17 test$line <- 2.5
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4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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18 second <- test
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19 second$cex <- 0.5
a4b734cd253b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
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20 second$line <- 2.5
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4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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22 do.trajectoryinspection.stemID <- function(ltr) { # nolint
a4b734cd253b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
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23 makeBranchLink <- function(i, j, k) { # nolint
a4b734cd253b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
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24 ingoing <- paste(sort(c(i, j)), collapse = ".")
a4b734cd253b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
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25 outgoing <- paste(sort(c(j, k)), collapse = ".")
a4b734cd253b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
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26 messed <- sort(c(ingoing, outgoing))
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4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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27 return(list(messed[[1]], messed[[2]]))
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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28 }
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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30 zzz <- do.call(getproj, c(ltr, trjsid.getproj))
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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31 bra <- branchcells(
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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32 ltr,
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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33 do.call("makeBranchLink", as.list(trjsid.branchcells.ijk))
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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34 )
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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35 write.table(
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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36 head(bra$diffgenes$z, trjsid.numdiffgenes),
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37 file = out.diffgenes)
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38
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39 par(mfrow = c(3, 2), cex = 0.5)
a4b734cd253b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
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40 print(do.call(plotmap, c(bra$scl, final = FALSE, fr = FALSE)))
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4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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41 print(do.call(mtext, c("Initial Clusters (tSNE)", test)))
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a4b734cd253b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
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42 print(do.call(plotmap, c(bra$scl, final = TRUE, fr = FALSE)))
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4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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43 print(do.call(mtext, c("Final Clusters (tSNE)", test)))
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44 print(do.call(plotmap, c(bra$scl, final = FALSE, um = TRUE)))
a4b734cd253b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
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45 print(do.call(mtext, c("Initial Clusters (UMAP)", test)))
a4b734cd253b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
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46 print(do.call(plotmap, c(bra$scl, final = TRUE, um = TRUE)))
a4b734cd253b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
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47 print(do.call(mtext, c("Final Clusters (UMAP)", test)))
a4b734cd253b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
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48 print(do.call(plotmap, c(bra$scl, final = FALSE, fr = TRUE)))
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4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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49 print(do.call(mtext, c("Initial Clusters (F-R)", test)))
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50 print(do.call(plotmap, c(bra$scl, final = TRUE, fr = TRUE)))
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4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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51 print(do.call(mtext, c("Final Clusters (F-R)", test)))
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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52 }
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53
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54 do.trajectoryinspection.fateID <- function(ltr) { # nolint
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55 n <- do.call(cellsfromtree, c(ltr, trjfid.cellsfrom))
4ea021bd7513 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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56 x <- getfdata(ltr@sc)
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57
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58 trjfid.filterset$x <- x
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59 trjfid.filterset$n <- n$f
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60 fs <- do.call(filterset, c(trjfid.filterset))
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61 trjfid.getsom$x <- fs
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62 s1d <- do.call(getsom, c(trjfid.getsom))
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63 trjfid.procsom$s1d <- s1d
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64 ps <- do.call(procsom, c(trjfid.procsom))
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65
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66 y <- ltr@sc@cpart[n$f]
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67 fcol <- ltr@sc@fcol
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68
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69 trjfid.plotheat$xpart <- y
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70 trjfid.plotheat$xcol <- fcol
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72 test$side <- 3
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73 test$line <- 3
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75 ##Plot average z-score for all modules derived from the SOM:
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76 trjfid.plotheat$x <- ps$nodes.z
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77 trjfid.plotheat$ypart <- unique(ps$nodes)
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78 print(do.call(plotheatmap, c(trjfid.plotheat)))
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79 print(do.call(mtext, c("Average z-score for all modules derived from SOM",
a4b734cd253b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
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80 test)))
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81 ##Plot z-score profile of each gene ordered by SOM modules:
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82 trjfid.plotheat$x <- ps$all.z
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83 trjfid.plotheat$ypart <- ps$nodes
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84 print(do.call(plotheatmap, c(trjfid.plotheat)))
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85 print(do.call(mtext, c(paste0("z-score profile of each gene",
a4b734cd253b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
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86 "ordered by SOM modules"), test)))
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87 ##Plot normalized expression profile of each gene ordered by SOM modules:
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88 trjfid.plotheat$x <- ps$all.e
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89 trjfid.plotheat$ypart <- ps$nodes
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90 print(do.call(plotheatmap, c(trjfid.plotheat)))
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91 print(do.call(mtext, c(paste0("Normalized expression profile of each",
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92 "gene ordered by SOM modules"), test)))
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93 ##Plot binarized expression profile of each gene
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94 ##(z-score < -1, -1 < z-score < 1, z-score > 1)
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95 trjfid.plotheat$x <- ps$all.b
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96 trjfid.plotheat$ypart <- ps$nodes
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97 print(do.call(plotheatmap, c(trjfid.plotheat)))
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98 print(do.call(mtext, c("Binarized expression profile of each gene", test)))
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99 ## This should be written out, and passed back into the tool
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100 ## to perform sominspect
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101 return(list(fs = fs, ps = ps, y = y, fcol = fcol, nf = n$f))
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102 }
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103
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104 do.trajectoryinspection.fateID.sominspect <- function(domo) { # nolint
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105 g <- trjfidsomi.use.genes
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106 if (class(g) == "numeric") {
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107 g <- names(ps$nodes)[ps$nodes %in% g]
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108 }
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109
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110 typ <- NULL
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111 if (!is.null(trjfidsomi.use.types)) {
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112 typ <- sub(trjfidsomi.use.types, "", domo$nf)
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113 }
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114
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115 trjfidsomi$x <- domo$fs
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116 trjfidsomi$y <- domo$y
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117 trjfidsomi$g <- g
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118 trjfidsomi$n <- domo$nf
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119 trjfidsomi$col <- domo$fcol
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120 trjfidsomi$types <- typ
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121
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122 ## The average pseudo-temporal expression profile of this group
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123 ## can be plotted by the function plotexpression:
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124 par(mfrow = c(1, 1))
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125 test$cex <- 1
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126 second$line <- 1.5
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127 if (trjfidsomi$name == "Title") trjfidsomi$name <- ""
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128 print(do.call(plotexpression, c(trjfidsomi)))
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129 mess2 <- paste(c(trjfidsomi.use.genes), collapse = ", ")
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130 mess1 <- "Average pseudo-temporal expression profile"
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131 print(do.call(mtext, c(mess1, test)))
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132 print(do.call(mtext, c(mess2, second)))
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133 }
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134
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135 ltr <- in.rdat
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136
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137 pdf(out.pdf)
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138 if (perform.stemID) do.trajectoryinspection.stemID(ltr)
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139 if (perform.fateID) {
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140 domo <- do.trajectoryinspection.fateID(ltr)
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141 if (perform.fateID.sominspect) {
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142 do.trajectoryinspection.fateID.sominspect(domo)
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143 }
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144 }
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145 dev.off()