Mercurial > repos > greg > ks_distribution

comparison ks_distribution.R @ 21:e6bbc7426cd1 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Mon, 26 Jun 2017 07:51:11 -0400
parents 79e00e063a40
children 492ef68d73f7
comparison
equal deleted inserted replaced
20:79e00e063a40 21:e6bbc7426cd1
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=[], 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 (length(colors) == 0)
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 {
94 items <- strsplit(cStr, ",") 94 items <- strsplit(cStr, ",")
95 for (item in items) { 95 for (item in items) {
96 color <- c(color, item) 96 color <- c(color, item)
97 } 97 }
98 num_colors_specified = length(color) 98 num_colors_specified = length(color)
99 if num_colors_specified < num_components: 99 if (num_colors_specified < num_components):
100 { 100 {
101 for (i in num_colors_specified:num_components) 101 for (i in num_colors_specified:num_components)
102 { 102 {
103 if !(any(color=='red') 103 if !(any(color=='red'))
104 { 104 {
105 color <- c(color, 'red') 105 color <- c(color, 'red')
106 } 106 }
107 else if !(any(color=='yellow') 107 else if !(any(color=='yellow'))
108 { 108 {
109 color <- c(color, 'yellow') 109 color <- c(color, 'yellow')
110 } 110 }
111 else if !(any(color=='green') 111 else if !(any(color=='green'))
112 { 112 {
113 color <- c(color, 'green') 113 color <- c(color, 'green')
114 } 114 }
115 else if !(any(color=='black') 115 else if !(any(color=='black'))
116 { 116 {
117 color <- c(color, 'black') 117 color <- c(color, 'black')
118 } 118 }
119 else if !(any(color=='blue') 119 else if !(any(color=='blue'))
120 { 120 {
121 color <- c(color, 'blue') 121 color <- c(color, 'blue')
122 } 122 }
123 else 123 else
124 { 124 {