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comparison ks_distribution.R @ 61:c19c48db9f79 draft

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author greg
date Tue, 27 Jun 2017 08:16:54 -0400
parents ae25785e78e1
children a9c1203d5eb6
comparison
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60:ae25785e78e1 61:c19c48db9f79
5 option_list <- list( 5 option_list <- list(
6 make_option(c("-c", "--components_input"), action="store", dest="components_input", help="Ks significant components input dataset"), 6 make_option(c("-c", "--components_input"), action="store", dest="components_input", help="Ks significant components input dataset"),
7 make_option(c("-k", "--kaks_input"), action="store", dest="kaks_input", help="KaKs analysis input dataset"), 7 make_option(c("-k", "--kaks_input"), action="store", dest="kaks_input", help="KaKs analysis input dataset"),
8 make_option(c("-n", "--number_comp"), action="store", dest="number_comp", type="integer", help="Number of significant components in the Ks distribution"), 8 make_option(c("-n", "--number_comp"), action="store", dest="number_comp", type="integer", help="Number of significant components in the Ks distribution"),
9 make_option(c("-o", "--output"), action="store", dest="output", help="Output dataset"), 9 make_option(c("-o", "--output"), action="store", dest="output", help="Output dataset"),
10 make_option(c("-s", "--specified_colors"), action="store", dest="specified_colors", default=NA, help="List of component colors") 10 make_option(c("-s", "--specified_colors"), action="store", dest="specified_colors", default=NULL, help="List of component colors")
11 ) 11 )
12 12
13 parser <- OptionParser(usage="%prog [options] file", option_list=option_list) 13 parser <- OptionParser(usage="%prog [options] file", option_list=option_list)
14 args <- parse_args(parser, positional_arguments=TRUE) 14 args <- parse_args(parser, positional_arguments=TRUE)
15 opt <- args$options 15 opt <- args$options
16 16
17 set_component_colors = function(colors, number_comp) 17 set_component_colors = function(colors, number_comp)
18 { 18 {
19 # Handle colors for components. 19 # Handle colors for components.
20 if (is.na(colors)) { 20 if (is.null(colors)) {
21 # Randomly specify colors for components. 21 # Randomly specify colors for components.
22 component_colors <- c('red', 'yellow', 'green', 'black', 'blue', 'darkorange') 22 component_colors <- c('red', 'yellow', 'green', 'black', 'blue', 'darkorange')
23 } else { 23 } else {
24 # Handle selected colors for components. 24 # Handle selected colors for components.
25 component_colors <- c() 25 component_colors <- c()