Mercurial > repos > iuc > raceid_inspectclusters

comparison scripts/clusterinspect.R @ 0:9fec5dd8fbb9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
author iuc
date Thu, 22 Nov 2018 04:45:41 -0500
parents
children 20f522154663
comparison
equal deleted inserted replaced
-1:000000000000 0:9fec5dd8fbb9
1 #!/usr/bin/env R
2 VERSION = "0.2"
3
4 args = commandArgs(trailingOnly = T)
5
6 if (length(args) != 1){
7 message(paste("VERSION:", VERSION))
8 stop("Please provide the config file")
9 }
10
11 suppressWarnings(suppressPackageStartupMessages(require(RaceID)))
12 source(args[1])
13
14 ## layout
15 test <- list()
16 test$side = 3
17 test$line = 3
18
19 do.plotting <- function(sc){
20 print(plotmap(sc, final = FALSE, fr = FALSE))
21 print(do.call(mtext, c("Initial Clustering tSNE", test)))
22 print(plotmap(sc, final = TRUE, fr = FALSE))
23 print(do.call(mtext, c("Final Clustering tSNE", test)))
24 print(plotmap(sc, final = FALSE, fr = TRUE))
25 print(do.call(mtext, c("Initial Clustering Fruchterman-Reingold", test)))
26 print(plotmap(sc, final = TRUE, fr = TRUE))
27 print(do.call(mtext, c("Final Clustering Fruchterman-Reingold", test)))
28 }
29
30
31 do.inspect.symbolmap <- function(sc){
32 if (!is.null(plotsym.use.typeremoveregex)){
33 plotsym$types = sub(plotsym.use.typeremoveregex, "", colnames(sc@ndata))
34
35 if (!is.null(plotsym.use.typeremoveregex.subselect)){
36 plotsym$subset = plotsym$types[grep(plotsym.use.typeremoveregex.subselect, plotsym$types)]
37 }
38 }
39 plotsym$fr = FALSE
40 print(do.call(plotsymbolsmap, c(sc, plotsym)))
41 print(do.call(mtext, c("Symbols tSNE", test)))
42 plotsym$fr = TRUE
43 print(do.call(plotsymbolsmap, c(sc, plotsym)))
44 print(do.call(mtext, c("Symbols FR", test)))
45 }
46
47 do.inspect.diffgene <- function(sc){
48
49 getSubNames <- function(lob, sc){
50 use.names <- NULL
51 if (!is.null(lob$manual)){
52 use.names <- lob$manual
53 }
54 else if (!is.null(lob$regex)){
55 nm <- colnames(sc@ndata)
56 use.names <- nm[grep(lob$regex, nm)]
57 }
58 else if (!is.null(lob$cln)){
59 use.names <- names(sc@cpart)[sc@cpart %in% lob$cln]
60 }
61 if (is.null(use.names)){
62 stop("A or B names not given!")
63 }
64 return(use.names)
65 }
66
67 A <- getSubNames(gfdat.A.use, sc)
68 B <- getSubNames(gfdat.B.use, sc)
69
70 fdat <- getfdata(sc, n=c(A,B))
71 dexp <- diffexpnb(fdat, A=A, B=B)
72 ## options for diffexpnb are mostly about DESeq, ignore
73 plotdiffg$x = dexp
74 print(do.call(plotdiffgenesnb, c(plotdiffg)))
75 print(do.call(mtext, c("Diff Genes", test)))
76 }
77
78
79 do.inspect.genesofinterest <- function(sc){
80 if (is.null(plotexp$n)){ ## No title, and one gene? Use gene name
81 if (length(plotexp$g) == 1){
82 plotexp$n <- plotexp$g
83 } else {
84 plotexp$n <- paste(plotexp$g, collapse=", ")
85 }
86 }
87
88 title <- paste(":", plotexp$n)
89 plotexp$n <- ""
90
91 plotexp$logsc=FALSE; plotexp$fr = FALSE
92 print(do.call(plotexpmap, c(sc, plotexp)))
93 print(do.call(mtext, c(paste("tSNE", title), test)))
94
95 plotexp$logsc=TRUE; plotexp$fr = FALSE
96 print(do.call(plotexpmap, c(sc, plotexp)))
97 print(do.call(mtext, c(paste("tSNE (Log)", title), test)))
98
99 plotexp$logsc=FALSE; plotexp$fr = TRUE
100 print(do.call(plotexpmap, c(sc, plotexp)))
101 print(do.call(mtext, c(paste("FR", title), test)))
102
103 plotexp$logsc=TRUE; plotexp$fr = TRUE
104 print(do.call(plotexpmap, c(sc, plotexp)))
105 print(do.call(mtext, c(paste("FR (Log)", title), test)))
106
107 if (!is.null(plotmarkg$samples)){
108 reg <- plotmarkg$samples
109 plotmarkg$samples <- sub("(\\_\\d+)$","", colnames(sc@ndata))
110 }
111 print(do.call(plotmarkergenes, c(sc, plotmarkg)))
112 }
113
114 sc <- in.rdat
115
116 pdf(out.pdf)
117 if (perform.plotting) do.plotting(sc)
118 if (perform.symbolmap) do.inspect.symbolmap(sc)
119 if (perform.genesofinterest) do.inspect.genesofinterest(sc)
120 if (perform.diffgene) do.inspect.diffgene(sc)
121 dev.off()