Mercurial > repos > iuc > pathview

comparison pathview.r @ 0:898228ced3fb draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043"
author iuc
date Mon, 26 Aug 2019 14:42:27 -0400
parents
children e9e98c810b7f
comparison
equal deleted inserted replaced
-1:000000000000 0:898228ced3fb
1 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
2
3 # we need that to not crash galaxy with an UTF8 error on German LC settings.
4 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
5
6 suppressPackageStartupMessages({
7 library("pathview")
8 library("optparse")
9 })
10
11 sessionInfo()
12
13 option_list <- list(
14 make_option(c("--pathway_id"), type="character", default=NULL, help="Path to tabular file with gene data"),
15 make_option(c("--pathway_id_fp"), type="character", default=NULL, help="Path to tabular file with pathway ids"),
16 make_option(c("--pathway_id_header"), type="logical", default=FALSE, help="Header for tabular file with pathway ids"),
17 make_option(c("--species"), type="character", default="hsa", help="KEGG code, scientific name or the common name of the species"),
18 make_option(c("--gene_data"), type="character", default=NULL, help="Path to tabular file with gene data"),
19 make_option(c("--gd_header"), type="logical", default=FALSE, help="Header for the gene data file"),
20 make_option(c("--gene_idtype"), type="character", default="entrez", help="ID type used for the gene data"),
21 make_option(c("--cpd_data"), type="character", default=NULL, help="Path to tabular file with compound data"),
22 make_option(c("--cpd_header"), type="logical", default=FALSE, help="Header for the compound data file"),
23 make_option(c("--cpd_idtype"), type="character", default="kegg", help="ID type used for the compound data"),
24 make_option(c("--multi_state"), type="logical", default=TRUE, help="Are the gene and compound data paired?"),
25 make_option(c("--match_data"), type="logical", default=TRUE, help="Are the gene and compound data paired?"),
26 make_option(c("--kegg_native"), type="logical", default=TRUE, help="Render pathway graph as native KEGG grap? Alternative is the Graphviz layout"),
27 make_option(c("--same_layer"), type="logical", default=TRUE, help="Plot on same layer?"),
28 make_option(c("--map_null"), type="logical", default=TRUE, help="Map the NULL gene or compound data to pathway?"),
29 make_option(c("--split_group"), type="logical", default=FALSE, help="Split node groups into individual nodes?"),
30 make_option(c("--expand_node"), type="logical", default=FALSE, help="Expand multiple-gene nodes into single-gene nodes?"),
31 make_option(c("--sign_pos"), type="character", default="bottomright", help="Position of pathview signature")
32 )
33
34 parser <- OptionParser(usage = "%prog [options] file", option_list=option_list)
35 args = parse_args(parser)
36 print(args)
37
38 read_table = function(fp, header, rownames=1, colclasses=NA){
39 table = read.table(fp, header=header, sep="\t", row.names=rownames, colClasses=colclasses)
40 # transform to vector if only one column
41 if(dim(table)[2] == 1){
42 names = rownames(table)
43 table = table[,1]
44 names(table) = names
45 }
46 return(table)
47 }
48
49 get_table = function(fp, header){
50 table = NULL
51 if(!is.null(fp)){
52 table = read_table(fp, header, rownames=1)
53 }
54 return(table)
55 }
56
57 # load gene_data file
58 gene_data = get_table(args$gene_data, args$gd_header)
59
60 # load compound data file
61 cpd_data = get_table(args$cpd_data, args$cpd_header)
62
63 run_pathview = function(pathway_id){
64 pathview(
65 pathway.id=pathway_id,
66 gene.data=gene_data,
67 gene.idtype=args$gene_idtype,
68 cpd.data=cpd_data,
69 cpd.idtype=args$cpd_idtype,
70 species=args$species,
71 multi.state=args$multi_state,
72 match.data=args$match_data,
73 kegg.native=args$kegg_native,
74 same.layer=args$same_layer,
75 split.group=args$split_group,
76 expand.node=args$expand_node,
77 sign.pos=args$sign_pos,
78 map.null=args$map_null)
79 }
80
81 # get pathway ids
82 if(!is.null(args$pathway_id)){
83 run_pathview(args$pathway_id)
84 } else {
85 pthws = read_table(args$pathway_id_fp, args$pathway_id_header, rownames=NULL, colclasses="character")
86 for(p in pthws){
87 run_pathview(p)
88 }
89 }