Mercurial > repos > iuc > raceid_inspecttrajectory
view scripts/pseudotemporal.R @ 8:df8e4e54d367 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 455bad7eca54164f95755174904842907846bb42"
author | iuc |
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date | Mon, 20 Dec 2021 10:11:41 +0000 |
parents | c8434a623268 |
children |
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#!/usr/bin/env R VERSION <- "0.1" # nolint args <- commandArgs(trailingOnly = T) # nolint if (length(args) != 1) { message(paste("VERSION:", VERSION)) stop("Please provide the config file") } suppressWarnings(suppressPackageStartupMessages(require(RaceID))) source(args[1]) test <- list() test$side <- 3 test$line <- 3 second <- test second$cex <- 0.5 second$line <- 2.5 do.pseudotemp <- function(sc) { # nolint pdf(out.pdf) ltr <- Ltree(sc) ltr <- compentropy(ltr) ltr <- do.call(projcells, c(ltr, pstc.projc)) ltr <- do.call(projback, c(ltr, pstc.projb)) ltr <- lineagegraph(ltr) ltr <- do.call(comppvalue, c(ltr, pstc.comppval)) x <- do.call(compscore, c(ltr, pstc.compscore)) print(do.call(mtext, c("Compute Score", test))) print(do.call(mtext, c(paste0("No. of inter-cluster links / ", "Delta median entropy of each cluster / ", "StemID2 score (combination of both)"), second))) plotdistanceratio(ltr) print(do.call(mtext, c("Cell-to-Cell Distance Ratio", test))) print(do.call(mtext, c("Original vs High-dimensional Embedded Space", second))) do.call(plotgraph, c(ltr, pstc.plotgraph)) print(do.call(mtext, c(paste0(c("Lineage Trajectories", rep(" ", 54)), collapse = ""), test))) print(do.call(mtext, c(paste0(c(paste0("Colour = Level of Significance, ", "Width = Link Score"), rep(" ", 106)), collapse = ""), second))) plotspantree(ltr) print(do.call(mtext, c("Minimum Spanning Tree", test))) plotspantree(ltr, projections = TRUE) print(do.call(mtext, c("Minimum Spanning Tree", test))) print(do.call(mtext, c("Cells Projected onto Links", second))) test$side <- 4 test$line <- 0 plotlinkscore(ltr) print(do.call(mtext, c("Link Score", test))) projenrichment(ltr) print(do.call(mtext, c("Enrichment Ratios", test))) dev.off() return(ltr) } ltr <- do.pseudotemp(in.rdat) saveRDS(ltr, out.rdat)