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comparison ks_distribution.R @ 60:ae25785e78e1 draft

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author greg
date Tue, 27 Jun 2017 08:06:19 -0400
parents 9ca7354c86a1
children c19c48db9f79
comparison
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59:c5fb4e2ed4e2 60:ae25785e78e1
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", dest="colors", default=NA, help="List of component colors") 10 make_option(c("-s", "--specified_colors"), action="store", dest="specified_colors", 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
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) == 0) { 20 if (is.na(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()
50 return(component_colors) 50 return(component_colors)
51 } 51 }
52 52
53 get_pi_mu_var = function(components_data, number_comp) 53 get_pi_mu_var = function(components_data, number_comp)
54 { 54 {
55 # FixMe: enhance this to generically handle any integer value for number_comp.
56 if (number_comp == 1) { 55 if (number_comp == 1) {
57 pi <- c(components_data[1, 9]) 56 pi <- c(components_data[1, 9])
58 mu <- c(components_data[1, 7]) 57 mu <- c(components_data[1, 7])
59 var <- c(components_data[1, 8]) 58 var <- c(components_data[1, 8])
60 } else if (number_comp == 2) { 59 } else if (number_comp == 2) {
134 # Read in the components data. 133 # Read in the components data.
135 components_data <- read.delim(opt$components_input, header=TRUE) 134 components_data <- read.delim(opt$components_input, header=TRUE)
136 number_comp <- as.integer(opt$number_comp) 135 number_comp <- as.integer(opt$number_comp)
137 136
138 # Set component colors. 137 # Set component colors.
139 component_colors <- set_component_colors(opt$colors, number_comp) 138 component_colors <- set_component_colors(opt$specified_colors, number_comp)
140 139
141 # Set pi, mu, var. 140 # Set pi, mu, var.
142 items <- get_pi_mu_var(components_data, number_comp) 141 items <- get_pi_mu_var(components_data, number_comp)
143 if (number_comp == 1) { 142 if (number_comp == 1) {
144 pi <- items[1] 143 pi <- items[1]