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comparison ks_distribution.R @ 64:b7468c75c4a5 draft

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author greg
date Tue, 27 Jun 2017 11:00:36 -0400
parents a9c1203d5eb6
children ad406d4702b2
comparison
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63:99ba4a5320e0 64:b7468c75c4a5
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()
84 } 84 }
85 results <- c(pi, mu, var) 85 results <- c(pi, mu, var)
86 return(results) 86 return(results)
87 } 87 }
88 88
89 plot_ks<-function(kaks_input, number_comp, component_colors, output, pi, mu, var) 89 plot_ks<-function(kaks_input, component_colors, output, pi, mu, var)
90 { 90 {
91 # Start PDF device driver to save charts to output. 91 # Start PDF device driver to save charts to output.
92 pdf(file=output, bg="white") 92 pdf(file=output, bg="white")
93 kaks <- read.table(file=kaks_input, header=T) 93 kaks <- read.table(file=kaks_input, header=T)
94 max_ks <- max(kaks$Ks, na.rm=TRUE) 94 max_ks <- max(kaks$Ks, na.rm=TRUE)
136 } 136 }
137 137
138 # Read in the components data. 138 # Read in the components data.
139 components_data <- read.delim(opt$components_input, header=TRUE) 139 components_data <- read.delim(opt$components_input, header=TRUE)
140 number_comp <- as.integer(opt$number_comp) 140 number_comp <- as.integer(opt$number_comp)
141 if (number_comp == 0) {
142 # Default to 1 component to allow functional testing.
143 number_comp <- 1
144 }
141 145
142 # Set component colors. 146 # Set component colors.
143 component_colors <- set_component_colors(opt$specified_colors, number_comp) 147 component_colors <- set_component_colors(opt$specified_colors, number_comp)
144 148
145 # Set pi, mu, var. 149 # Set pi, mu, var.
166 var <- items[11:15] 170 var <- items[11:15]
167 } else if (number_comp == 6) { 171 } else if (number_comp == 6) {
168 pi <- items[1:6] 172 pi <- items[1:6]
169 mu <- items[7:12] 173 mu <- items[7:12]
170 var <- items[13:18] 174 var <- items[13:18]
171 }
172 175
173 # Plot the output. 176 # Plot the output.
174 plot_ks(opt$kaks_input, number_comp, component_colors, opt$output, pi, mu, var) 177 plot_ks(opt$kaks_input, component_colors, opt$output, pi, mu, var)