Mercurial > repos > kuyt002 > vennerable_r
changeset 1:2d8c23e32839 default tip
2015-04-21 fixed <NA> values bug
| author | eric |
|---|---|
| date | Wed, 22 Apr 2015 10:35:33 +0200 |
| parents | f21d51d28d8d |
| children | |
| files | vennerable/Vennerable.R vennerable/Vennerable.xml |
| diffstat | 2 files changed, 30 insertions(+), 23 deletions(-) [+] |
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--- a/vennerable/Vennerable.R Tue Mar 31 13:18:31 2015 +0200 +++ b/vennerable/Vennerable.R Wed Apr 22 10:35:33 2015 +0200 @@ -2,19 +2,24 @@ # R script to call Vennerable package from galaxy # info: alex.bossers@wur.nl +# +# version: +# 2015-04-21 fixed <NA> values bug +# .......... Initial version +# # R --slave --vanilla --file=PlotBar.R --args inputFile x_data weighting outputFile plottype resolution imagetype # 1 2 3 4 5 6 7 8 9 10 11 12 #get cmd line args args <- commandArgs() - in.file <- args[6] - xData <- args[7] # data labels xData of format "a, b, c" and can include spaces - weighting <- args[8] - out.file <- args[9] - plottype <- args[10] - resolution <- args[11] # in dpi - imagetype <- args[12] # svg, pdf or png +in.file <- args[6] +xData <- args[7] # data labels xData of format "a, b, c" and can include spaces +weighting <- args[8] +out.file <- args[9] +plottype <- args[10] +resolution <- args[11] # in dpi +imagetype <- args[12] # svg, pdf or png #open lib library(Vennerable) @@ -23,12 +28,14 @@ # for labels of bars or bar groups presume column names from data if (xData != "default") { # read without header input file (must be tabular) - annot_data <- read.table(in.file, header=F, sep="\t") - colnames (annot_data) <- strsplit(xData,",")[[1]] + a_data <- read.delim(in.file, header=F, na.strings="") # replace empty by <NA> for TAB delimited file + colnames (a_data) <- strsplit(xData,",")[[1]] # insert headers from galaxy input + annot_data <- lapply(a_data, na.omit) # remove empty values for counting Vannot <- Venn(annot_data) } else { - # read without header input file (must be tabular) - annot_data <- read.table(in.file, header=T, sep="\t") + # read with header input file (must be tabular) + a_data <- read.delim(in.file, na.strings="") # replace any empty values by <NA> for AB delimited headered file + annot_data <- lapply(a_data, na.omit) # remove empty values for counting Vannot <- Venn(annot_data) } @@ -36,32 +43,32 @@ #R 3.0.2 and default cairo libs should handle it all ok #it could be that X11 should be loaded for non-pdf if (imagetype == "svg") { - svg(out.file) + svg(out.file) } else if (imagetype == "png") { - png(out.file, width = 1600, height = 1600, res = resolution) + png(out.file, width = 1600, height = 1600, res = resolution) } else { - pdf(out.file) + pdf(out.file) } # plot it if (plottype == "ChowRuskey") { plot(Vannot, type = plottype) - + } else if (plottype == "AWFE") { plot(Vannot, doWeights = weighting, type = plottype) - + } else if (plottype == "circles") { plot(Vannot) - + } else if (plottype == "ellipses"){ plot(Vannot, type = "ellipses") - + } else if (plottype == "squares"){ plot(Vannot, type = "squares") - + } else if (plottype == "battle"){ - plot(Vannot, type = "battle") + plot(Vannot, type = "battle") } -cat ("Wrapper version 1.2, running Vennerable v3.0-82\n Info/bugs: alex.bossers@wur.nl\n") -dev.off() +cat ("Wrapper version 1.2c (empty value bug fixed), running Vennerable v3.0-82\n Info/bugs: alex.bossers@wur.nl\n") +dev.off() \ No newline at end of file