Mercurial > repos > ethevenot > heatmap

comparison heatmap_wrapper.R @ 0:ad06aeed02c9 draft

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planemo upload for repository https://github.com/workflow4metabolomics/heatmap.git commit 7e599d006e53fefb7e1b923ba8894b4fb19f9cfa-dirty
author ethevenot
date Tue, 02 Aug 2016 06:26:41 -0400
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children b1667c118127
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-1:000000000000 0:ad06aeed02c9
1 #!/usr/bin/env Rscript
2
3 library(batch) ## parseCommandArgs
4
5 source_local <- function(fname){
6 argv <- commandArgs(trailingOnly = FALSE)
7 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
8 source(paste(base_dir, fname, sep="/"))
9 }
10
11 source_local("heatmap_script.R")
12
13 argVc <- unlist(parseCommandArgs(evaluate=FALSE))
14
15
16 ##------------------------------
17 ## Initializing
18 ##------------------------------
19
20 ## options
21 ##--------
22
23 strAsFacL <- options()[["stringsAsFactors"]]
24 options(stringsAsFactors=FALSE)
25
26 ## constants
27 ##----------
28
29 modNamC <- "Heatmap" ## module name
30
31 ## log file
32 ##---------
33
34 sink(argVc["information"])
35
36 cat("\nStart of the '", modNamC, "' module: ",
37 format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")
38
39 ## loading
40 ##--------
41
42 proMN <- t(as.matrix(read.table(argVc["dataMatrix_in"],
43 check.names = FALSE,
44 header = TRUE,
45 row.names = 1,
46 sep = "\t")))
47
48 obsDF <- read.table(argVc["sampleMetadata_in"],
49 check.names = FALSE,
50 header = TRUE,
51 row.names = 1,
52 sep = "\t")
53
54 feaDF <- read.table(argVc["variableMetadata_in"],
55 check.names = FALSE,
56 header = TRUE,
57 row.names = 1,
58 sep = "\t")
59
60 ## adding default parameter values
61 ##--------------------------------
62
63
64 if(!("corMetC" %in% names(argVc)))
65 argVc["corMetC"] <- "pearson"
66 if(!("aggMetC" %in% names(argVc)))
67 argVc["aggMetC"] <- "ward"
68 if(!("colC" %in% names(argVc)))
69 argVc["colC"] <- "blueOrangeRed"
70 if(!("scaL" %in% names(argVc)))
71 argVc["scaL"] <- "TRUE"
72 if(!("cexN" %in% names(argVc)))
73 argVc["cexN"] <- "0.8"
74
75 ## checking
76 ##---------
77
78 if(as.numeric(argVc["cutSamN"]) > nrow(proMN))
79 stop("Number of sample clusters must be inferior to the number of samples")
80 if(as.numeric(argVc["cutVarN"]) > ncol(proMN))
81 stop("Number of variable clusters must be inferior to the number of variables")
82
83 ## printing arguments
84 ##-------------------
85
86 cat("\nArguments used:\n\n")
87 argMC <- as.matrix(argVc)
88 colnames(argMC) <- "value"
89 argDatVl <- grepl("\\.dat$", argVc) ## discarding dataset file names
90 if(sum(argDatVl))
91 argMC <- argMC[!argDatVl, , drop = FALSE]
92 print(argMC)
93
94
95 ##------------------------------
96 ## Computation
97 ##------------------------------
98
99
100 heaLs <- heatmapF(proMN = proMN,
101 obsDF = obsDF,
102 feaDF = feaDF,
103 disC = argVc["disC"],
104 cutSamN = as.numeric(argVc["cutSamN"]),
105 cutVarN = as.numeric(argVc["cutVarN"]),
106 fig.pdfC = argVc["figure"],
107 corMetC = argVc["corMetC"],
108 aggMetC = argVc["aggMetC"],
109 colC = argVc["colC"],
110 scaL = as.logical(argVc["scaL"]),
111 cexN = as.numeric(argVc["cexN"]))
112
113
114 ##------------------------------
115 ## Ending
116 ##------------------------------
117
118
119 ## saving
120 ##-------
121
122 proDF <- cbind.data.frame(dataMatrix = colnames(heaLs[["proMN"]]),
123 as.data.frame(t(heaLs[["proMN"]])))
124 write.table(proDF,
125 file = argVc["dataMatrix_out"],
126 quote = FALSE,
127 row.names = FALSE,
128 sep = "\t")
129
130 obsDF <- cbind.data.frame(sampleMetadata = rownames(heaLs[["obsDF"]]),
131 heaLs[["obsDF"]])
132 write.table(obsDF,
133 file = argVc["sampleMetadata_out"],
134 quote = FALSE,
135 row.names = FALSE,
136 sep = "\t")
137
138 feaDF <- cbind.data.frame(variableMetadata = rownames(heaLs[["feaDF"]]),
139 heaLs[["feaDF"]])
140 write.table(feaDF,
141 file = argVc["variableMetadata_out"],
142 quote = FALSE,
143 row.names = FALSE,
144 sep = "\t")
145
146 ## Ending
147 ##-------
148
149 cat("\nEnd of the '", modNamC, "' Galaxy module call: ",
150 format(Sys.time(), "%a %d %b %Y %X"), "\n", sep = "")
151
152 sink()
153
154 options(stringsAsFactors = strAsFacL)
155
156 rm(list = ls())