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comparison mytools/Start_GenometriCorr.R @ 7:f0dc65e7f6c0

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author xuebing
date Fri, 09 Mar 2012 19:59:07 -0500
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6:094f377db4e5 7:f0dc65e7f6c0
1 # Start_GenometriCorr.R
2
3 ###################################################
4 # #
5 # command-line interface to GenometriCorr #
6 # functions, for use with Galaxy. #
7 # #
8 ###################################################
9
10 capture.output <- function (result, pdffile, output_options)
11 {
12 if(output_options != "stats")
13 {
14 pdf(file=pdffile, width=10, height=19, paper="special")
15
16 if (output_options != "vis") #need to do a plot
17 {
18 mymat <- matrix(ncol=3, nrow=4)
19 mymat[1,1] <- 1
20 mymat[1,2] <- 2
21 mymat[1,3] <- 3
22 mymat[2,1] <- 4
23 mymat[2,2] <- 5
24 mymat[2,3] <- 6
25 mymat[3,1] <- 7
26 mymat[3,2] <- 8
27 mymat[3,3] <- 9
28 mymat[4,1] <- 10
29 mymat[4,2] <- 11
30 mymat[4,3] <- 12
31
32 layout(mymat, heights=c(0.2,0.2,0.2,0.2))
33 plot(result, pdffile, make.new=FALSE)
34 }
35 if (output_options != "plot") #need to do the bigger graphic
36 {
37 mymat <- matrix(ncol=2, nrow=8)
38 mymat[1,1] <- 2
39 mymat[1,2] <- 3
40 mymat[2,1] <- 4
41 mymat[2,2] <- 4
42 mymat[3,1] <- 1
43 mymat[3,2] <- 1
44 mymat[4,1] <- 5
45 mymat[4,2] <- 6
46 mymat[5,1] <- 7
47 mymat[5,2] <- 7
48 mymat[6,1] <- 8
49 mymat[6,2] <- 9
50 mymat[7,1] <- 10
51 mymat[7,2] <- 10
52 mymat[8,1] <- 11
53 mymat[8,2] <- 12
54 layoutresults <- 3
55
56 layout(mymat, heights=c(0.05,0.05,0.15,0.15,0.15,0.15,0.15,0.15))
57 visualize(result, pdffile, make.new=FALSE)
58 }
59 dev.off()
60 }
61
62 if (output_options == "stats")
63 {
64 show(result)
65 }
66 }
67
68
69
70 # Reads the command line arguments
71 args <- commandArgs(trailingOnly=T)
72
73 suppressPackageStartupMessages(library('GenometriCorr', warn.conflicts=F, verbose=F))
74 suppressPackageStartupMessages(library('graphics', warn.conflicts=F, verbose=F))
75 suppressPackageStartupMessages(library('gdata', warn.conflicts=F, verbose=F))
76 suppressPackageStartupMessages(library('gplots', warn.conflicts=F, verbose=F))
77 suppressPackageStartupMessages(library('gtools', warn.conflicts=F, verbose=F))
78 suppressPackageStartupMessages(library('caTools', warn.conflicts=F, verbose=F))
79 suppressPackageStartupMessages(library('grid', warn.conflicts=F, verbose=F))
80
81
82
83 # Variables
84 query_file <- ""
85 reference_file <- ""
86 config_file <- ""
87 output_options <- ""
88
89 # Parse the command line arguments
90
91 config_file <- args[1]
92 query_file <- as.character(args[2])
93 reference_file <- as.character(args[3])
94 output_options <- args[4]
95 pdffile <- args[5]
96
97 conf<-new("GenometriCorrConfig",config_file)
98
99 print('OK')
100
101 result<-suppressWarnings(suppressPackageStartupMessages(GenometriCorr:::run.config(conf,query=query_file,reference=reference_file)))
102 print('OK2')
103
104 hideoutput <- capture.output(result, pdffile=args[5], output_options)
105