Mercurial > repos > iuc > raceid_inspecttrajectory

annotate scripts/pseudotemporal.R @ 10:6e90c8adf84f draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 0ffa71ef9f8d020fe7ba94502db8cec26fd8741f
author iuc
date Tue, 05 Nov 2024 16:33:56 +0000
parents c8434a623268
children
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e0e9b24d76aa 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 <- "0.1" # nolint
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3
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4 args <- commandArgs(trailingOnly = T) # nolint
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6 if (length(args) != 1) {
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7 message(paste("VERSION:", VERSION))
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8 stop("Please provide the config file")
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9 }
e0e9b24d76aa 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)))
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12 source(args[1])
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e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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14 test <- list()
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15 test$side <- 3
c8434a623268 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
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16 test$line <- 3
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17 second <- test
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18 second$cex <- 0.5
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19 second$line <- 2.5
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21
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22 do.pseudotemp <- function(sc) { # nolint
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23 pdf(out.pdf)
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24 ltr <- Ltree(sc)
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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25 ltr <- compentropy(ltr)
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26 ltr <- do.call(projcells, c(ltr, pstc.projc))
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27 ltr <- do.call(projback, c(ltr, pstc.projb))
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28 ltr <- lineagegraph(ltr)
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29 ltr <- do.call(comppvalue, c(ltr, pstc.comppval))
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30 x <- do.call(compscore, c(ltr, pstc.compscore))
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31 print(do.call(mtext, c("Compute Score", test)))
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32 print(do.call(mtext, c(
6e90c8adf84f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 0ffa71ef9f8d020fe7ba94502db8cec26fd8741f
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33 paste0(
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34 "No. of inter-cluster links / ",
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35 "Delta median entropy of each cluster / ",
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36 "StemID2 score (combination of both)"
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37 ),
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38 second
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39 )))
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40 plotdistanceratio(ltr)
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41 print(do.call(mtext, c("Cell-to-Cell Distance Ratio", test)))
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42 print(do.call(mtext, c(
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43 "Original vs High-dimensional Embedded Space",
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44 second
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45 )))
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46 do.call(plotgraph, c(ltr, pstc.plotgraph))
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47 print(do.call(mtext, c(paste0(c("Lineage Trajectories", rep(" ", 54)),
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48 collapse = ""
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49 ), test)))
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50 print(do.call(mtext, c(paste0(c(
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51 paste0(
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52 "Colour = Level of Significance, ",
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53 "Width = Link Score"
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54 ),
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55 rep(" ", 106)
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56 ), collapse = ""), second)))
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57 plotspantree(ltr)
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58 print(do.call(mtext, c("Minimum Spanning Tree", test)))
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59 plotspantree(ltr, projections = TRUE)
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60 print(do.call(mtext, c("Minimum Spanning Tree", test)))
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61 print(do.call(mtext, c("Cells Projected onto Links", second)))
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62 test$side <- 4
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63 test$line <- 0
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64 plotlinkscore(ltr)
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65 print(do.call(mtext, c("Link Score", test)))
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66 projenrichment(ltr)
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67 print(do.call(mtext, c("Enrichment Ratios", test)))
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68 dev.off()
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69
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70 return(ltr)
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71 }
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73 ltr <- do.pseudotemp(in.rdat)
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75
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76 saveRDS(ltr, out.rdat)