Mercurial > repos > iuc > raceid_inspecttrajectory
annotate scripts/clusterinspect.R @ 10:6e90c8adf84f draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 0ffa71ef9f8d020fe7ba94502db8cec26fd8741f
author | iuc |
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date | Tue, 05 Nov 2024 16:33:56 +0000 |
parents | a6821f856a1e |
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rev | line source |
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e0e9b24d76aa
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 |
10
6e90c8adf84f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 0ffa71ef9f8d020fe7ba94502db8cec26fd8741f
iuc
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2 VERSION <- "0.5" # nolint |
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e0e9b24d76aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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3 |
9
a6821f856a1e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 82a18e57158136e265a26f27feb40f8dc13437bf
iuc
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4 args <- commandArgs(trailingOnly = TRUE) |
0
e0e9b24d76aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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5 |
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c8434a623268
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
iuc
parents:
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6 if (length(args) != 1) { |
10
6e90c8adf84f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 0ffa71ef9f8d020fe7ba94502db8cec26fd8741f
iuc
parents:
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7 message(paste("VERSION:", VERSION)) |
6e90c8adf84f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 0ffa71ef9f8d020fe7ba94502db8cec26fd8741f
iuc
parents:
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8 stop("Please provide the config file") |
0
e0e9b24d76aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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9 } |
e0e9b24d76aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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10 |
e0e9b24d76aa
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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11 suppressWarnings(suppressPackageStartupMessages(require(RaceID))) |
e0e9b24d76aa
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]) |
e0e9b24d76aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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13 |
e0e9b24d76aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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14 ## layout |
e0e9b24d76aa
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() |
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c8434a623268
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
iuc
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16 test$side <- 3 |
c8434a623268
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
iuc
parents:
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17 test$line <- 3 |
0
e0e9b24d76aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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18 |
6
c8434a623268
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
iuc
parents:
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19 do.plotting <- function(sc) { # nolint |
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86e2358cf273
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
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20 |
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c8434a623268
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
iuc
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21 sc_tmp <- sc |
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86e2358cf273
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
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22 |
86e2358cf273
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
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23 ## If it's a subset, we need to get clever and subset specific parts |
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c8434a623268
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
iuc
parents:
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24 if (!(is.null(plotting.cln) || is.na(plotting.cln))) { |
c8434a623268
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
iuc
parents:
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25 cellstokeep <- names(sc_tmp@cpart[sc_tmp@cpart %in% plotting.cln]) |
4
86e2358cf273
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
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26 |
86e2358cf273
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
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27 ## Subselect partitions for initial and final clusters |
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c8434a623268
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
iuc
parents:
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28 sc_tmp@cpart <- sc_tmp@cpart[cellstokeep] |
c8434a623268
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
iuc
parents:
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29 sc_tmp@cluster$kpart <- sc_tmp@cluster$kpart[cellstokeep] |
4
86e2358cf273
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
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30 |
86e2358cf273
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
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31 ## Subselect tSNE and FR data |
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c8434a623268
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
iuc
parents:
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32 sc_tmp@tsne <- sc_tmp@tsne[colnames(sc_tmp@ndata) %in% cellstokeep, ] |
c8434a623268
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
iuc
parents:
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33 sc_tmp@umap <- sc_tmp@umap[colnames(sc_tmp@ndata) %in% cellstokeep, ] |
c8434a623268
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
iuc
parents:
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34 sc_tmp@fr <- sc_tmp@fr[cellstokeep, ] |
4
86e2358cf273
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
0
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35 } |
86e2358cf273
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
iuc
parents:
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36 |
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c8434a623268
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
iuc
parents:
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37 print(plotmap(sc_tmp, final = FALSE, fr = FALSE)) |
0
e0e9b24d76aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
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38 print(do.call(mtext, c("Initial Clustering tSNE", test))) |
6
c8434a623268
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
iuc
parents:
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39 print(plotmap(sc_tmp, final = TRUE, fr = FALSE)) |
0
e0e9b24d76aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
diff
changeset
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40 print(do.call(mtext, c("Final Clustering tSNE", test))) |
6
c8434a623268
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
iuc
parents:
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41 print(plotmap(sc_tmp, final = FALSE, um = TRUE)) |
c8434a623268
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
iuc
parents:
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42 print(do.call(mtext, c("Initial Clustering UMAP", test))) |
c8434a623268
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
iuc
parents:
4
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43 print(plotmap(sc_tmp, final = TRUE, um = TRUE)) |
c8434a623268
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
iuc
parents:
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44 print(do.call(mtext, c("Final Clustering UMAP", test))) |
c8434a623268
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
iuc
parents:
4
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45 print(plotmap(sc_tmp, final = FALSE, fr = TRUE)) |
0
e0e9b24d76aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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46 print(do.call(mtext, c("Initial Clustering Fruchterman-Reingold", test))) |
6
c8434a623268
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
iuc
parents:
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47 print(plotmap(sc_tmp, final = TRUE, fr = TRUE)) |
0
e0e9b24d76aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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48 print(do.call(mtext, c("Final Clustering Fruchterman-Reingold", test))) |
e0e9b24d76aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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49 } |
e0e9b24d76aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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50 |
e0e9b24d76aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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51 |
10
6e90c8adf84f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 0ffa71ef9f8d020fe7ba94502db8cec26fd8741f
iuc
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52 do.inspect.symbolmap <- function(sc) { # nolint |
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c8434a623268
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
iuc
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53 if (!is.null(plotsym.use.typeremoveregex)) { |
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6e90c8adf84f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 0ffa71ef9f8d020fe7ba94502db8cec26fd8741f
iuc
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54 plotsym$types <- sub( |
6e90c8adf84f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 0ffa71ef9f8d020fe7ba94502db8cec26fd8741f
iuc
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55 plotsym.use.typeremoveregex, "", |
6e90c8adf84f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 0ffa71ef9f8d020fe7ba94502db8cec26fd8741f
iuc
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56 colnames(sc@ndata) |
6e90c8adf84f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 0ffa71ef9f8d020fe7ba94502db8cec26fd8741f
iuc
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57 ) |
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e0e9b24d76aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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58 |
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c8434a623268
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
iuc
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59 if (!is.null(plotsym.use.typeremoveregex.subselect)) { |
c8434a623268
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
iuc
parents:
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60 plotsym$subset <- plotsym$types[grep( |
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6e90c8adf84f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 0ffa71ef9f8d020fe7ba94502db8cec26fd8741f
iuc
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61 plotsym.use.typeremoveregex.subselect, |
6e90c8adf84f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 0ffa71ef9f8d020fe7ba94502db8cec26fd8741f
iuc
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62 plotsym$types |
6e90c8adf84f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 0ffa71ef9f8d020fe7ba94502db8cec26fd8741f
iuc
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63 )] |
0
e0e9b24d76aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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64 } |
e0e9b24d76aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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65 } |
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c8434a623268
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
iuc
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66 plotsym$fr <- FALSE |
0
e0e9b24d76aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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67 print(do.call(plotsymbolsmap, c(sc, plotsym))) |
e0e9b24d76aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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68 print(do.call(mtext, c("Symbols tSNE", test))) |
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c8434a623268
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
iuc
parents:
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69 plotsym$fr <- TRUE |
0
e0e9b24d76aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
parents:
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70 print(do.call(plotsymbolsmap, c(sc, plotsym))) |
e0e9b24d76aa
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(mtext, c("Symbols FR", test))) |
e0e9b24d76aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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72 } |
e0e9b24d76aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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73 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 0ffa71ef9f8d020fe7ba94502db8cec26fd8741f
iuc
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74 do.inspect.diffgene <- function(sc) { # nolint |
0
e0e9b24d76aa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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75 |
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6e90c8adf84f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 0ffa71ef9f8d020fe7ba94502db8cec26fd8741f
iuc
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76 getSubNames <- function(lob, sc) { # nolint |
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c8434a623268
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
iuc
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77 use_names <- NULL |
c8434a623268
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
iuc
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78 if (!is.null(lob$manual)) { |
c8434a623268
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79 use_names <- lob$manual |
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80 } else if (!is.null(lob$regex)) { |
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81 nm <- colnames(sc@ndata) |
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82 use_names <- nm[grep(lob$regex, nm)] |
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83 } else if (!is.null(lob$cln)) { |
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84 use_names <- names(sc@cpart)[sc@cpart %in% lob$cln] |
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85 } |
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86 if (is.null(use_names)) { |
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87 stop("A or B names not given!") |
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88 } |
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89 return(use_names) |
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90 } |
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91 |
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92 A <- getSubNames(gfdat.A.use, sc) # nolint |
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93 B <- getSubNames(gfdat.B.use, sc) # nolint |
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94 |
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95 fdat <- getfdata(sc, n = c(A, B)) |
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96 dexp <- diffexpnb(fdat, A = A, B = B) |
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97 ## options for diffexpnb are mostly about DESeq, ignore |
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98 plotdiffg$x <- dexp |
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99 print(do.call(plotdiffgenesnb, c(plotdiffg))) |
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100 print(do.call(mtext, c("Diff Genes", test))) |
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101 } |
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102 |
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103 |
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104 do.inspect.genesofinterest <- function(sc) { # nolint |
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105 if (is.null(plotexp$n)) { ## No title, and one gene? Use gene name |
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106 if (length(plotexp$g) == 1) { |
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107 plotexp$n <- plotexp$g |
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108 } else { |
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109 plotexp$n <- paste(plotexp$g, collapse = ", ") |
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110 } |
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111 } |
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112 |
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113 title <- paste(":", plotexp$n) |
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114 plotexp$n <- "" |
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115 |
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116 plotexp$logsc <- FALSE |
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117 plotexp$fr <- FALSE |
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118 print(do.call(plotexpmap, c(sc, plotexp))) |
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119 print(do.call(mtext, c(paste("tSNE", title), test))) |
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120 |
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121 plotexp$logsc <- TRUE |
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122 plotexp$fr <- FALSE |
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123 print(do.call(plotexpmap, c(sc, plotexp))) |
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124 print(do.call(mtext, c(paste("tSNE (Log)", title), test))) |
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125 |
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126 plotexp$logsc <- FALSE |
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127 plotexp$fr <- TRUE |
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128 print(do.call(plotexpmap, c(sc, plotexp))) |
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129 print(do.call(mtext, c(paste("FR", title), test))) |
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130 |
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131 plotexp$logsc <- TRUE |
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132 plotexp$fr <- TRUE |
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133 print(do.call(plotexpmap, c(sc, plotexp))) |
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134 print(do.call(mtext, c(paste("FR (Log)", title), test))) |
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135 |
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136 if (!is.null(plotmarkg$samples)) { |
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137 reg <- plotmarkg$samples |
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138 plotmarkg$samples <- sub("(\\_\\d+)$", "", colnames(sc@ndata)) |
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139 } |
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140 print(do.call(plotmarkergenes, c(sc, plotmarkg))) |
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141 } |
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142 |
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143 sc <- in.rdat |
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144 |
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145 pdf(out.pdf) |
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146 if (perform.plotting) do.plotting(sc) |
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147 if (perform.symbolmap) do.inspect.symbolmap(sc) |
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148 if (perform.genesofinterest) do.inspect.genesofinterest(sc) |
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149 if (perform.diffgene) do.inspect.diffgene(sc) |
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150 dev.off() |