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comparison ks_distribution.R @ 42:60e2cf57f2c1 draft

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author greg
date Mon, 26 Jun 2017 12:10:21 -0400
parents 17ca41359a2d
children 5074cb26597a
comparison
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41:17ca41359a2d 42:60e2cf57f2c1
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("-r", "--colors"), action="store", default=NA, help="List of component colors") 10 make_option(c("-r", "--colors"), action="store", default="", 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 (nchar(colors) == 0)
21 { 21 {
22 # Randomly specify colors for components. 22 # Randomly specify colors for components.
23 specified_colors <- c('red', 'yellow', 'green', 'black', 'blue', 'darkorange') 23 specified_colors <- c('red', 'yellow', 'green', 'black', 'blue', 'darkorange')
24 } 24 }
25 else 25 else