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comparison ks_distribution.R @ 20:79e00e063a40 draft

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author greg
date Fri, 23 Jun 2017 15:00:42 -0400
parents 828b43bcf2ac
children e6bbc7426cd1
comparison
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19:14f771140d45 20:79e00e063a40
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", "--num_comp"), action="store", dest="num_comp", type="integer", help="Number of significant components in the Ks distribution"), 8 make_option(c("-n", "--num_comp"), action="store", dest="num_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=NA, 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
80 vx <- seq(1, 100) * (max_ks / 100) 80 vx <- seq(1, 100) * (max_ks / 100)
81 ymax <- max(nc) 81 ymax <- max(nc)
82 barplot(nc, space=0.25, offset=0, width=0.04, xlim=c(0, max_ks), ylim=c(0, ymax), col="lightpink1", border="lightpink3") 82 barplot(nc, space=0.25, offset=0, width=0.04, xlim=c(0, max_ks), ylim=c(0, ymax), col="lightpink1", border="lightpink3")
83 # Add x-axis. 83 # Add x-axis.
84 axis(1) 84 axis(1)
85 if(is.na(colors) 85 if is.na(colors)
86 { 86 {
87 color <- c('red', 'yellow', 'green', 'black', 'blue', 'darkorange') 87 color <- c('red', 'yellow', 'green', 'black', 'blue', 'darkorange')
88 } 88 }
89 else 89 else
90 { 90 {