Mercurial > repos > iuc > raceid_trajectory
comparison scripts/pseudotemporal.R @ 10:2bfd55b87af3 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 0ffa71ef9f8d020fe7ba94502db8cec26fd8741f
| author | iuc |
|---|---|
| date | Tue, 05 Nov 2024 16:34:11 +0000 |
| parents | 72979cac22b2 |
| children |
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| 9:2af7c5086a96 | 10:2bfd55b87af3 |
|---|---|
| 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))) |