--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/pseudotemporal.R	Thu Nov 22 04:45:41 2018 -0500
@@ -0,0 +1,58 @@
+#!/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)