--- a/scripts/pseudotemporal.R	Wed Jan 29 17:16:02 2020 -0500
+++ b/scripts/pseudotemporal.R	Thu Apr 15 19:00:38 2021 +0000
@@ -1,9 +1,9 @@
 #!/usr/bin/env R
-VERSION = "0.1"
+VERSION <- "0.1" # nolint
 
-args = commandArgs(trailingOnly = T)
+args <- commandArgs(trailingOnly = T) # nolint
 
-if (length(args) != 1){
+if (length(args) != 1) {
      message(paste("VERSION:", VERSION))
      stop("Please provide the config file")
 }
@@ -12,37 +12,44 @@
 source(args[1])
 
 test <- list()
-test$side = 3
-test$line = 3
+test$side <- 3
+test$line <- 3
 second <- test
-second$cex = 0.5
-second$line = 2.5
+second$cex <- 0.5
+second$line <- 2.5
 
 
-do.pseudotemp <- function(sc){
+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))    
+    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)))
+    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)))
+    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)))
+    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)))
-    plotprojections(ltr)
+    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
+    test$side <- 4
+    test$line <- 0
     plotlinkscore(ltr)
     print(do.call(mtext, c("Link Score", test)))
     projenrichment(ltr)