Mercurial > repos > iuc > raceid_inspecttrajectory

comparison scripts/pseudotemporal.R @ 0:e0e9b24d76aa draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
author iuc
date Thu, 22 Nov 2018 04:42:18 -0500
parents
children c8434a623268
comparison
equal deleted inserted replaced
-1:000000000000 0:e0e9b24d76aa
1 #!/usr/bin/env R
2 VERSION = "0.1"
3
4 args = commandArgs(trailingOnly = T)
5
6 if (length(args) != 1){
7 message(paste("VERSION:", VERSION))
8 stop("Please provide the config file")
9 }
10
11 suppressWarnings(suppressPackageStartupMessages(require(RaceID)))
12 source(args[1])
13
14 test <- list()
15 test$side = 3
16 test$line = 3
17 second <- test
18 second$cex = 0.5
19 second$line = 2.5
20
21
22 do.pseudotemp <- function(sc){
23 pdf(out.pdf)
24 ltr <- Ltree(sc)
25 ltr <- compentropy(ltr)
26 ltr <- do.call(projcells, c(ltr, pstc.projc))
27 ltr <- do.call(projback, c(ltr, pstc.projb))
28 ltr <- lineagegraph(ltr)
29 ltr <- do.call(comppvalue, c(ltr, pstc.comppval))
30 x <- do.call(compscore, c(ltr, pstc.compscore))
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)))
33 plotdistanceratio(ltr)
34 print(do.call(mtext, c("Cell-to-Cell Distance Ratio", test)))
35 print(do.call(mtext, c("Original vs High-dimensional Embedded Space", second)))
36 do.call(plotgraph, c(ltr, pstc.plotgraph))
37 print(do.call(mtext, c("Lineage Trajectories ", test)))
38 print(do.call(mtext, c("Colour = Level of Significance, Width = Link Score ", second)))
39 plotspantree(ltr)
40 print(do.call(mtext, c("Minimum Spanning Tree", test)))
41 plotprojections(ltr)
42 print(do.call(mtext, c("Minimum Spanning Tree", test)))
43 print(do.call(mtext, c("Cells Projected onto Links", second)))
44 test$side = 4
45 test$line = 0
46 plotlinkscore(ltr)
47 print(do.call(mtext, c("Link Score", test)))
48 projenrichment(ltr)
49 print(do.call(mtext, c("Enrichment Ratios", test)))
50 dev.off()
51
52 return(ltr)
53 }
54
55 ltr <- do.pseudotemp(in.rdat)
56
57
58 saveRDS(ltr, out.rdat)