Mercurial > repos > iuc > raceid_inspecttrajectory

comparison scripts/trajectoryinspect.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 a6821f856a1e
children
comparison
equal deleted inserted replaced
9:a6821f856a1e 10:6e90c8adf84f
2 VERSION <- "0.2" # nolint 2 VERSION <- "0.2" # nolint
3 3
4 args <- commandArgs(trailingOnly = TRUE) 4 args <- commandArgs(trailingOnly = TRUE)
5 5
6 if (length(args) != 1) { 6 if (length(args) != 1) {
7 message(paste("VERSION:", VERSION)) 7 message(paste("VERSION:", VERSION))
8 stop("Please provide the config file") 8 stop("Please provide the config file")
9 } 9 }
10 10
11 suppressWarnings(suppressPackageStartupMessages(require(RaceID))) 11 suppressWarnings(suppressPackageStartupMessages(require(RaceID)))
12 suppressWarnings(suppressPackageStartupMessages(require(FateID))) 12 suppressWarnings(suppressPackageStartupMessages(require(FateID)))
13 source(args[1]) 13 source(args[1])
32 ltr, 32 ltr,
33 do.call("makeBranchLink", as.list(trjsid.branchcells.ijk)) 33 do.call("makeBranchLink", as.list(trjsid.branchcells.ijk))
34 ) 34 )
35 write.table( 35 write.table(
36 head(bra$diffgenes$z, trjsid.numdiffgenes), 36 head(bra$diffgenes$z, trjsid.numdiffgenes),
37 file = out.diffgenes) 37 file = out.diffgenes
38 )
38 39
39 par(mfrow = c(3, 2), cex = 0.5) 40 par(mfrow = c(3, 2), cex = 0.5)
40 print(do.call(plotmap, c(bra$scl, final = FALSE, fr = FALSE))) 41 print(do.call(plotmap, c(bra$scl, final = FALSE, fr = FALSE)))
41 print(do.call(mtext, c("Initial Clusters (tSNE)", test))) 42 print(do.call(mtext, c("Initial Clusters (tSNE)", test)))
42 print(do.call(plotmap, c(bra$scl, final = TRUE, fr = FALSE))) 43 print(do.call(plotmap, c(bra$scl, final = TRUE, fr = FALSE)))
61 trjfid_getsom$x <- fs 62 trjfid_getsom$x <- fs
62 s1d <- do.call(getsom, c(trjfid_getsom)) 63 s1d <- do.call(getsom, c(trjfid_getsom))
63 trjfid_procsom$s1d <- s1d 64 trjfid_procsom$s1d <- s1d
64 ps <- do.call(procsom, c(trjfid_procsom)) 65 ps <- do.call(procsom, c(trjfid_procsom))
65 66
66 y <- ltr@sc@cpart[n$f] 67 y <- ltr@sc@cpart[n$f]
67 fcol <- ltr@sc@fcol 68 fcol <- ltr@sc@fcol
68 69
69 trjfid_plotheat$xpart <- y 70 trjfid_plotheat$xpart <- y
70 trjfid_plotheat$xcol <- fcol 71 trjfid_plotheat$xcol <- fcol
71 72
72 test$side <- 3 73 test$side <- 3
73 test$line <- 3 74 test$line <- 3
74 75
75 ##Plot average z-score for all modules derived from the SOM: 76 ## Plot average z-score for all modules derived from the SOM:
76 trjfid_plotheat$x <- ps$nodes.z 77 trjfid_plotheat$x <- ps$nodes.z
77 trjfid_plotheat$ypart <- unique(ps$nodes) 78 trjfid_plotheat$ypart <- unique(ps$nodes)
78 print(do.call(plotheatmap, c(trjfid_plotheat))) 79 print(do.call(plotheatmap, c(trjfid_plotheat)))
79 print(do.call(mtext, c("Average z-score for all modules derived from SOM", 80 print(do.call(mtext, c(
80 test))) 81 "Average z-score for all modules derived from SOM",
81 ##Plot z-score profile of each gene ordered by SOM modules: 82 test
83 )))
84 ## Plot z-score profile of each gene ordered by SOM modules:
82 trjfid_plotheat$x <- ps$all.z 85 trjfid_plotheat$x <- ps$all.z
83 trjfid_plotheat$ypart <- ps$nodes 86 trjfid_plotheat$ypart <- ps$nodes
84 print(do.call(plotheatmap, c(trjfid_plotheat))) 87 print(do.call(plotheatmap, c(trjfid_plotheat)))
85 print(do.call(mtext, c(paste0("z-score profile of each gene", 88 print(do.call(mtext, c(paste0(
86 "ordered by SOM modules"), test))) 89 "z-score profile of each gene",
87 ##Plot normalized expression profile of each gene ordered by SOM modules: 90 "ordered by SOM modules"
91 ), test)))
92 ## Plot normalized expression profile of each gene ordered by SOM modules:
88 trjfid_plotheat$x <- ps$all.e 93 trjfid_plotheat$x <- ps$all.e
89 trjfid_plotheat$ypart <- ps$nodes 94 trjfid_plotheat$ypart <- ps$nodes
90 print(do.call(plotheatmap, c(trjfid_plotheat))) 95 print(do.call(plotheatmap, c(trjfid_plotheat)))
91 print(do.call(mtext, c(paste0("Normalized expression profile of each", 96 print(do.call(mtext, c(paste0(
92 "gene ordered by SOM modules"), test))) 97 "Normalized expression profile of each",
93 ##Plot binarized expression profile of each gene 98 "gene ordered by SOM modules"
94 ##(z-score < -1, -1 < z-score < 1, z-score > 1) 99 ), test)))
100 ## Plot binarized expression profile of each gene
101 ## (z-score < -1, -1 < z-score < 1, z-score > 1)
95 trjfid_plotheat$x <- ps$all.b 102 trjfid_plotheat$x <- ps$all.b
96 trjfid_plotheat$ypart <- ps$nodes 103 trjfid_plotheat$ypart <- ps$nodes
97 print(do.call(plotheatmap, c(trjfid_plotheat))) 104 print(do.call(plotheatmap, c(trjfid_plotheat)))
98 print(do.call(mtext, c("Binarized expression profile of each gene", test))) 105 print(do.call(mtext, c("Binarized expression profile of each gene", test)))
99 ## This should be written out, and passed back into the tool 106 ## This should be written out, and passed back into the tool