Mercurial > repos > iuc > raceid_inspectclusters

comparison scripts/pseudotemporal.R @ 10:c7ddb719554d 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 16:33:10 +0000
parents 41f34e925bd5
children
comparison
equal deleted inserted replaced
9:f3eb2291da05 10:c7ddb719554d
2 VERSION <- "0.1" # nolint 2 VERSION <- "0.1" # nolint
3 3
4 args <- commandArgs(trailingOnly = T) # nolint 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
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(paste0("No. of inter-cluster links / ", 32 print(do.call(mtext, c(
33 "Delta median entropy of each cluster / ", 33 paste0(
34 "StemID2 score (combination of both)"), 34 "No. of inter-cluster links / ",
35 second))) 35 "Delta median entropy of each cluster / ",
36 "StemID2 score (combination of both)"
37 ),
38 second
39 )))
36 plotdistanceratio(ltr) 40 plotdistanceratio(ltr)
37 print(do.call(mtext, c("Cell-to-Cell Distance Ratio", test))) 41 print(do.call(mtext, c("Cell-to-Cell Distance Ratio", test)))
38 print(do.call(mtext, c("Original vs High-dimensional Embedded Space", 42 print(do.call(mtext, c(
39 second))) 43 "Original vs High-dimensional Embedded Space",
44 second
45 )))
40 do.call(plotgraph, c(ltr, pstc.plotgraph)) 46 do.call(plotgraph, c(ltr, pstc.plotgraph))
41 print(do.call(mtext, c(paste0(c("Lineage Trajectories", rep(" ", 54)), 47 print(do.call(mtext, c(paste0(c("Lineage Trajectories", rep(" ", 54)),
42 collapse = ""), test))) 48 collapse = ""
43 print(do.call(mtext, c(paste0(c(paste0("Colour = Level of Significance, ", 49 ), test)))
44 "Width = Link Score"), 50 print(do.call(mtext, c(paste0(c(
45 rep(" ", 106)), collapse = ""), second))) 51 paste0(
52 "Colour = Level of Significance, ",
53 "Width = Link Score"
54 ),
55 rep(" ", 106)
56 ), collapse = ""), second)))
46 plotspantree(ltr) 57 plotspantree(ltr)
47 print(do.call(mtext, c("Minimum Spanning Tree", test))) 58 print(do.call(mtext, c("Minimum Spanning Tree", test)))
48 plotspantree(ltr, projections = TRUE) 59 plotspantree(ltr, projections = TRUE)
49 print(do.call(mtext, c("Minimum Spanning Tree", test))) 60 print(do.call(mtext, c("Minimum Spanning Tree", test)))
50 print(do.call(mtext, c("Cells Projected onto Links", second))) 61 print(do.call(mtext, c("Cells Projected onto Links", second)))