Mercurial > repos > iuc > raceid_clustering

comparison scripts/pseudotemporal.R @ 6:a4b734cd253b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
author iuc
date Thu, 15 Apr 2021 18:58:21 +0000
parents 4ea021bd7513
children
comparison
equal deleted inserted replaced
5:7e014059a88d 6:a4b734cd253b
1 #!/usr/bin/env R 1 #!/usr/bin/env R
2 VERSION = "0.1" 2 VERSION <- "0.1" # nolint
3 3
4 args = commandArgs(trailingOnly = T) 4 args <- commandArgs(trailingOnly = T) # nolint
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 source(args[1]) 12 source(args[1])
13 13
14 test <- list() 14 test <- list()
15 test$side = 3 15 test$side <- 3
16 test$line = 3 16 test$line <- 3
17 second <- test 17 second <- test
18 second$cex = 0.5 18 second$cex <- 0.5
19 second$line = 2.5 19 second$line <- 2.5
20 20
21 21
22 do.pseudotemp <- function(sc){ 22 do.pseudotemp <- function(sc) { # nolint
23 pdf(out.pdf) 23 pdf(out.pdf)
24 ltr <- Ltree(sc) 24 ltr <- Ltree(sc)
25 ltr <- compentropy(ltr) 25 ltr <- compentropy(ltr)
26 ltr <- do.call(projcells, c(ltr, pstc.projc)) 26 ltr <- do.call(projcells, c(ltr, pstc.projc))
27 ltr <- do.call(projback, c(ltr, pstc.projb)) 27 ltr <- do.call(projback, c(ltr, pstc.projb))
28 ltr <- lineagegraph(ltr) 28 ltr <- lineagegraph(ltr)
29 ltr <- do.call(comppvalue, c(ltr, pstc.comppval)) 29 ltr <- do.call(comppvalue, c(ltr, pstc.comppval))
30 x <- do.call(compscore, c(ltr, pstc.compscore)) 30 x <- do.call(compscore, c(ltr, pstc.compscore))
31 print(do.call(mtext, c("Compute Score", test))) 31 print(do.call(mtext, c("Compute Score", test)))
32 print(do.call(mtext, c("No. of inter-cluster links / Delta median entropy of each cluster / StemID2 score (combination of both)", second))) 32 print(do.call(mtext, c(paste0("No. of inter-cluster links / ",
33 "Delta median entropy of each cluster / ",
34 "StemID2 score (combination of both)"),
35 second)))
33 plotdistanceratio(ltr) 36 plotdistanceratio(ltr)
34 print(do.call(mtext, c("Cell-to-Cell Distance Ratio", test))) 37 print(do.call(mtext, c("Cell-to-Cell Distance Ratio", test)))
35 print(do.call(mtext, c("Original vs High-dimensional Embedded Space", second))) 38 print(do.call(mtext, c("Original vs High-dimensional Embedded Space",
39 second)))
36 do.call(plotgraph, c(ltr, pstc.plotgraph)) 40 do.call(plotgraph, c(ltr, pstc.plotgraph))
37 print(do.call(mtext, c("Lineage Trajectories ", test))) 41 print(do.call(mtext, c(paste0(c("Lineage Trajectories", rep(" ", 54)),
38 print(do.call(mtext, c("Colour = Level of Significance, Width = Link Score ", second))) 42 collapse = ""), test)))
43 print(do.call(mtext, c(paste0(c(paste0("Colour = Level of Significance, ",
44 "Width = Link Score"),
45 rep(" ", 106)), collapse = ""), second)))
39 plotspantree(ltr) 46 plotspantree(ltr)
40 print(do.call(mtext, c("Minimum Spanning Tree", test))) 47 print(do.call(mtext, c("Minimum Spanning Tree", test)))
41 plotprojections(ltr) 48 plotspantree(ltr, projections = TRUE)
42 print(do.call(mtext, c("Minimum Spanning Tree", test))) 49 print(do.call(mtext, c("Minimum Spanning Tree", test)))
43 print(do.call(mtext, c("Cells Projected onto Links", second))) 50 print(do.call(mtext, c("Cells Projected onto Links", second)))
44 test$side = 4 51 test$side <- 4
45 test$line = 0 52 test$line <- 0
46 plotlinkscore(ltr) 53 plotlinkscore(ltr)
47 print(do.call(mtext, c("Link Score", test))) 54 print(do.call(mtext, c("Link Score", test)))
48 projenrichment(ltr) 55 projenrichment(ltr)
49 print(do.call(mtext, c("Enrichment Ratios", test))) 56 print(do.call(mtext, c("Enrichment Ratios", test)))
50 dev.off() 57 dev.off()