Mercurial > repos > stevecassidy > vowelplot
view phonR_tool.R @ 3:24f05f509f09 draft
planemo upload commit e4adec77d8b4e6385b7db85ebbe01cfb85ed8de2
author | stevecassidy |
---|---|
date | Fri, 14 Oct 2016 15:07:25 -0400 |
parents | 3d068b7441be |
children |
line wrap: on
line source
# # Galaxy tool that plots Vowels using the phonR package. # Accepts 8 inputs of the form <tsv data file> <output file name> <column1> <column2> <optPretty> <optEllipse> <optTokens> <optMeans> # Created by Michael Bauer # library(phonR) library(getopt) #create options option_specification = matrix(c( 'pdffile', 'h', 1, 'character', 'inputfile', 'i', 1, 'character', 'column1', 'y', 1, 'integer', 'column2', 'z', 1, 'integer', 'columnvowels', 'x', 1, 'integer', 'pretty', 'p', 1, 'logical', 'ellipse', 'e', 1, 'logical', 'tokens', 't', 1, 'logical', 'means', 'm', 1, 'logical', 'cextokens', 'c', 1, 'numeric', 'alphatokens', 'a', 1, 'numeric', 'cexmeans', 'b', 1, 'numeric' ), byrow=TRUE, ncol=4); # Parse options options = getopt(option_specification); pdffile <- gsub("[ ]+", "", paste(options$pdffile)) data = read.table(options$inputfile,sep="\t", header=TRUE); pdf(pdffile); plotVowels(data[,options$column1], data[,options$column2], data[,options$columnvowels], plot.tokens = options$tokens, pch.tokens = data[,options$columnvowels], cex.tokens = options$cextokens, alpha.tokens = options$alphatokens, plot.means = options$means, pch.means = data[,options$columnvowels], cex.means = options$cexmeans, var.col.by = data[,options$columnvowels], ellipse.line = options$ellipse, pretty = options$pretty) dev.off();