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comparison ks_distribution.R @ 62:a9c1203d5eb6 draft

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author greg
date Tue, 27 Jun 2017 09:02:48 -0400
parents c19c48db9f79
children b7468c75c4a5
comparison
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61:c19c48db9f79 62:a9c1203d5eb6
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.null(colors)) { 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()
26 colors <- as.character(colors) 26 colors <- as.character(colors)
27 items <- strsplit(colors, ",") 27 items <- strsplit(colors, ",")
28 for (item in items) { 28 for (item in items) {
29 component_colors <- c(component_colors, item) 29 component_colors <- c(component_colors, item)
30 } 30 }
31 num_colors_specified <- length(component_colors) 31 num_colors_specified <- length(component_colors)
32 if (num_colors_specified < number_comp) { 32 if (num_colors_specified < number_comp) {
33 for (i in num_colors_specified:number_comp) { 33 # The number of selected colors is less than the number of
34 if (!('red' %in% names(component_colors))) { 34 # components, so we'll add random colors that were not
35 component_colors <- c(component_colors, 'red') 35 # selected to the set of component colors until we have a
36 } else if (!('yellow' %in% names(component_colors))) { 36 # color for each component.
37 component_colors <- c(component_colors, 'yellow') 37 loop_count <- number_comp - num_colors_specified
38 } else if (!('green' %in% names(component_colors))) { 38 for (i in 1:loop_count) {
39 component_colors <- c(component_colors, 'green') 39 if (!(is.element("red", component_colors))) {
40 } else if (!('black' %in% names(component_colors))) { 40 component_colors <- c(component_colors, "red")
41 component_colors <- c(component_colors, 'black') 41 } else if (!(is.element("yellow", component_colors))) {
42 } else if (!('blue' %in% names(component_colors))) { 42 component_colors <- c(component_colors, "yellow")
43 component_colors <- c(component_colors, 'blue') 43 } else if (!(is.element("green", component_colors))) {
44 } else { 44 component_colors <- c(component_colors, "green")
45 component_colors <- c(component_colors, 'darkorange') 45 } else if (!(is.element("black", component_colors))) {
46 component_colors <- c(component_colors, "black")
47 } else if (!(is.element("blue", component_colors))) {
48 component_colors <- c(component_colors, "blue")
49 } else if (!(is.element("darkorange", component_colors))) {
50 component_colors <- c(component_colors, "darkorange")
46 } 51 }
47 } 52 }
48 } 53 }
49 } 54 }
50 return(component_colors) 55 return(component_colors)
138 component_colors <- set_component_colors(opt$specified_colors, number_comp) 143 component_colors <- set_component_colors(opt$specified_colors, number_comp)
139 144
140 # Set pi, mu, var. 145 # Set pi, mu, var.
141 items <- get_pi_mu_var(components_data, number_comp) 146 items <- get_pi_mu_var(components_data, number_comp)
142 if (number_comp == 1) { 147 if (number_comp == 1) {
143 pi <- items[1] 148 pi <- items[1]
144 mu <- items[2] 149 mu <- items[2]
145 var <- items[3] 150 var <- items[3]
146 } else if (number_comp == 2) { 151 } else if (number_comp == 2) {
147 pi <- items[1:2] 152 pi <- items[1:2]
148 mu <- items[3:4] 153 mu <- items[3:4]
149 var <- items[5:6] 154 var <- items[5:6]
150 } else if (number_comp == 3) { 155 } else if (number_comp == 3) {
151 pi <- items[1:3] 156 pi <- items[1:3]
152 mu <- items[4:6] 157 mu <- items[4:6]
153 var <- items[7:9] 158 var <- items[7:9]
154 } else if (number_comp == 4) { 159 } else if (number_comp == 4) {
155 pi <- items[1:4] 160 pi <- items[1:4]
156 mu <- items[5:8] 161 mu <- items[5:8]
157 var <- items[9:12] 162 var <- items[9:12]
158 } else if (number_comp == 5) { 163 } else if (number_comp == 5) {
159 pi <- items[1:5] 164 pi <- items[1:5]
160 mu <- items[6:10] 165 mu <- items[6:10]
161 var <- items[11:15] 166 var <- items[11:15]
162 } else if (number_comp == 6) { 167 } else if (number_comp == 6) {
163 pi <- items[1:6] 168 pi <- items[1:6]
164 mu <- items[7:12] 169 mu <- items[7:12]
165 var <- items[13:18] 170 var <- items[13:18]
166 } 171 }
167 172
168 # Plot the output. 173 # Plot the output.
169 plot_ks(opt$kaks_input, number_comp, component_colors, opt$output, pi, mu, var) 174 plot_ks(opt$kaks_input, number_comp, component_colors, opt$output, pi, mu, var)