comparison ggplotscripthistogram.R @ 5:097e19ec0150 draft

Uploaded

4:25c690797274

  'transform', 'c', 2, 'character',
  'woutputdim', 'w', 2, 'integer',
  'houtputdim', 'd', 2, 'integer',
  'dim', 'k', 2, 'character',
  'scaling', 'j', 2, 'character',
  'output', 'o', 2, 'character'
  ), byrow=TRUE, ncol=4);

# Parse options
options = getopt(option_specification);

cat("\n output: ",options$output)

integrated <- read.csv(options$input,sep='\t',header=TRUE)
input <- melt(integrated)


#Choose between automatically scaled x and y axis or user defined
if(options$scaling == "Automatic"){
    gg_scalex = NULL
    gg_scaley = NULL

    gg_colorscale = scale_color_brewer(palette=options$colors, direction=options$colororder)
  }

ggplot(input,aes(value,color=variable)) +
geom_freqpoly(binwidth=options$binwidth,size=options$size)+gg_facet+gg_colorscale+
gg_scalex+gg_scaley+theme_bw()+xlab(options$xlab)+ylab(options$ylab)+
ggtitle(options$title)

ggsave(file=options$output)

5:097e19ec0150

  'transform', 'c', 2, 'character',
  'woutputdim', 'w', 2, 'integer',
  'houtputdim', 'd', 2, 'integer',
  'dim', 'k', 2, 'character',
  'scaling', 'j', 2, 'character',
  'legend', 'l', 2, 'character',
  'output', 'o', 2, 'character'
  ), byrow=TRUE, ncol=4);

# Parse options
options = getopt(option_specification);

cat("\n output: ",options$output)

integrated <- read.csv(options$input,sep='\t',header=TRUE)
input <- melt(integrated)

gg_legend = show.legend=options$legend

#Choose between automatically scaled x and y axis or user defined
if(options$scaling == "Automatic"){
    gg_scalex = NULL
    gg_scaley = NULL

    gg_colorscale = scale_color_brewer(palette=options$colors, direction=options$colororder)
  }

ggplot(input,aes(value,color=variable)) +
geom_freqpoly(binwidth=options$binwidth,size=options$size)+gg_facet+gg_colorscale+
gg_scalex+gg_scaley+theme_bw()+xlab(options$xlab)+ylab(options$ylab)+gg_legend+
ggtitle(options$title)

ggsave(file=options$output)