Mercurial > repos > iuc > raceid_inspectclusters

comparison scripts/clusterinspect.R @ 4:20f522154663 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 5d7c4cd914295a81d42bf8baaad4981c23a83059"
author iuc
date Mon, 12 Aug 2019 13:01:12 -0400
parents 9fec5dd8fbb9
children 41f34e925bd5
comparison
equal deleted inserted replaced
3:0fa80752a314 4:20f522154663
1 #!/usr/bin/env R 1 #!/usr/bin/env R
2 VERSION = "0.2" 2 VERSION = "0.5"
3 3
4 args = commandArgs(trailingOnly = T) 4 args = commandArgs(trailingOnly = T)
5 5
6 if (length(args) != 1){ 6 if (length(args) != 1){
7 message(paste("VERSION:", VERSION)) 7 message(paste("VERSION:", VERSION))
15 test <- list() 15 test <- list()
16 test$side = 3 16 test$side = 3
17 test$line = 3 17 test$line = 3
18 18
19 do.plotting <- function(sc){ 19 do.plotting <- function(sc){
20 print(plotmap(sc, final = FALSE, fr = FALSE)) 20
21 sc.tmp <- sc
22
23 ## If it's a subset, we need to get clever and subset specific parts
24 if (!(is.null(plotting.cln) || is.na(plotting.cln))){
25 cellstokeep <- names(sc.tmp@cpart[sc.tmp@cpart %in% plotting.cln])
26
27 ## Subselect partitions for initial and final clusters
28 sc.tmp@cpart <- sc.tmp@cpart[cellstokeep]
29 sc.tmp@cluster$kpart <- sc.tmp@cluster$kpart[cellstokeep]
30
31 ## Subselect tSNE and FR data
32 ## - Note: no names in tsne, so we assume it follows the ndata naming
33 sc.tmp@tsne <- sc.tmp@tsne[colnames(sc.tmp@ndata) %in% cellstokeep,]
34 sc.tmp@fr <- sc.tmp@fr[cellstokeep,]
35 }
36
37 print(plotmap(sc.tmp, final = FALSE, fr = FALSE))
21 print(do.call(mtext, c("Initial Clustering tSNE", test))) 38 print(do.call(mtext, c("Initial Clustering tSNE", test)))
22 print(plotmap(sc, final = TRUE, fr = FALSE)) 39 print(plotmap(sc.tmp, final = TRUE, fr = FALSE))
23 print(do.call(mtext, c("Final Clustering tSNE", test))) 40 print(do.call(mtext, c("Final Clustering tSNE", test)))
24 print(plotmap(sc, final = FALSE, fr = TRUE)) 41 print(plotmap(sc.tmp, final = FALSE, fr = TRUE))
25 print(do.call(mtext, c("Initial Clustering Fruchterman-Reingold", test))) 42 print(do.call(mtext, c("Initial Clustering Fruchterman-Reingold", test)))
26 print(plotmap(sc, final = TRUE, fr = TRUE)) 43 print(plotmap(sc.tmp, final = TRUE, fr = TRUE))
27 print(do.call(mtext, c("Final Clustering Fruchterman-Reingold", test))) 44 print(do.call(mtext, c("Final Clustering Fruchterman-Reingold", test)))
28 } 45 }
29 46
30 47
31 do.inspect.symbolmap <- function(sc){ 48 do.inspect.symbolmap <- function(sc){