Mercurial > repos > iuc > raceid_trajectory
view scripts/pseudotemporal.R @ 1:30d9118a650a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 71e6b205841c83391ea8fc69e10eac03f212f4d6
author | iuc |
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date | Thu, 28 Feb 2019 12:59:30 -0500 |
parents | ff7cd3c7c1df |
children | 72979cac22b2 |
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#!/usr/bin/env R VERSION = "0.1" args = commandArgs(trailingOnly = T) 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){ 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("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("Lineage Trajectories ", test))) print(do.call(mtext, c("Colour = Level of Significance, Width = Link Score ", second))) plotspantree(ltr) print(do.call(mtext, c("Minimum Spanning Tree", test))) plotprojections(ltr) 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)