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comparison ks_distribution.R @ 51:1a3973eea61c draft

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author greg
date Mon, 26 Jun 2017 14:33:04 -0400
parents 0b3d12ecce28
children 53bc81f3ebad
comparison
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50:0b3d12ecce28 51:1a3973eea61c
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) == 0) {
21 # Randomly specify colors for components. 21 # Randomly specify colors for components.
22 specified_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 colors <- as.character(colors) 25 colors <- as.character(colors)
26 specified_colors <- strsplit(colors, ",") 26 component_colors <- strsplit(colors, ",")
27 num_colors_specified <- length(specified_colors) 27 num_colors_specified <- length(component_colors)
28 if (num_colors_specified < number_comp) { 28 if (num_colors_specified < number_comp) {
29 for (i in num_colors_specified:number_comp) { 29 for (i in num_colors_specified:number_comp) {
30 if (!('red' %in% names(specified_colors))) { 30 if (!('red' %in% names(component_colors))) {
31 specified_colors <- c(specified_colors, 'red') 31 component_colors <- c(component_colors, 'red')
32 } else if (!('yellow' %in% names(specified_colors))) { 32 } else if (!('yellow' %in% names(component_colors))) {
33 specified_colors <- c(specified_colors, 'yellow') 33 component_colors <- c(component_colors, 'yellow')
34 } else if (!('green' %in% names(specified_colors))) { 34 } else if (!('green' %in% names(component_colors))) {
35 specified_colors <- c(specified_colors, 'green') 35 component_colors <- c(component_colors, 'green')
36 } else if (!('black' %in% names(specified_colors))) { 36 } else if (!('black' %in% names(component_colors))) {
37 specified_colors <- c(specified_colors, 'black') 37 component_colors <- c(component_colors, 'black')
38 } else if (!('blue' %in% names(specified_colors))) { 38 } else if (!('blue' %in% names(component_colors))) {
39 specified_colors <- c(specified_colors, 'blue') 39 component_colors <- c(component_colors, 'blue')
40 } else { 40 } else {
41 specified_colors <- c(specified_colors, 'darkorange') 41 component_colors <- c(component_colors, 'darkorange')
42 } 42 }
43 } 43 }
44 } 44 }
45 } 45 }
46 return(specified_colors) 46 return(component_colors)
47 } 47 }
48 48
49 get_pi_mu_var = function(components_data, number_comp) 49 get_pi_mu_var = function(components_data, number_comp)
50 { 50 {
51 # FixMe: enhance this to generically handle any integer value for number_comp. 51 # FixMe: enhance this to generically handle any integer value for number_comp.
72 } else if (number_comp == 6) { 72 } else if (number_comp == 6) {
73 pi <- c(components_data[16, 9], components_data[17, 9], components_data[18, 9], components_data[19, 9], components_data[20, 9], components_data[21, 9]) 73 pi <- c(components_data[16, 9], components_data[17, 9], components_data[18, 9], components_data[19, 9], components_data[20, 9], components_data[21, 9])
74 mu <- c(components_data[16, 7], components_data[17, 7], components_data[18, 7], components_data[19, 7], components_data[20, 7], components_data[21, 7]) 74 mu <- c(components_data[16, 7], components_data[17, 7], components_data[18, 7], components_data[19, 7], components_data[20, 7], components_data[21, 7])
75 var <- c(components_data[16, 8], components_data[17, 8], components_data[18, 8], components_data[19, 8], components_data[20, 8], components_data[21, 8]) 75 var <- c(components_data[16, 8], components_data[17, 8], components_data[18, 8], components_data[19, 8], components_data[20, 8], components_data[21, 8])
76 } 76 }
77 results = c(pi, mu, var) 77 results <- c(pi, mu, var)
78 return(results) 78 return(results)
79 } 79 }
80 80
81 plot_ks<-function(kaks_input, number_comp, specified_colors, output, pi, mu, var) 81 plot_ks<-function(kaks_input, number_comp, component_colors, output, pi, mu, var)
82 { 82 {
83 # Start PDF device driver to save charts to output. 83 # Start PDF device driver to save charts to output.
84 pdf(file=output, bg="white") 84 pdf(file=output, bg="white")
85 kaks <- read.table(file=kaks_input, header=T) 85 kaks <- read.table(file=kaks_input, header=T)
86 max_ks <- max(kaks$Ks, na.rm=TRUE) 86 max_ks <- max(kaks$Ks, na.rm=TRUE)
102 ymax <- max(nc) 102 ymax <- max(nc)
103 barplot(nc, space=0.25, offset=0, width=0.04, xlim=c(0, max_ks), ylim=c(0, ymax), col="lightpink1", border="lightpink3") 103 barplot(nc, space=0.25, offset=0, width=0.04, xlim=c(0, max_ks), ylim=c(0, ymax), col="lightpink1", border="lightpink3")
104 # Add x-axis. 104 # Add x-axis.
105 axis(1) 105 axis(1)
106 for (i in 1:length(mu)) { 106 for (i in 1:length(mu)) {
107 lines(vx, g[,i] * h, lwd=2, col=specified_colors[i]) 107 lines(vx, g[,i] * h, lwd=2, col=component_colors[i])
108 } 108 }
109 } 109 }
110 110
111 calculate_fitted_density <- function(pi, mu, var, max_ks) 111 calculate_fitted_density <- function(pi, mu, var, max_ks)
112 { 112 {
130 # Read in the components data. 130 # Read in the components data.
131 components_data <- read.delim(opt$components_input, header=TRUE) 131 components_data <- read.delim(opt$components_input, header=TRUE)
132 number_comp <- as.integer(opt$number_comp) 132 number_comp <- as.integer(opt$number_comp)
133 133
134 # Set component colors. 134 # Set component colors.
135 specified_colors <- set_component_colors(opt$colors, number_comp) 135 component_colors <- set_component_colors(opt$colors, number_comp)
136 136
137 # Set pi, mu, var. 137 # Set pi, mu, var.
138 items <- get_pi_mu_var(components_data, number_comp) 138 items <- get_pi_mu_var(components_data, number_comp)
139 if (number_comp == 1) { 139 if (number_comp == 1) {
140 pi <- items[1] 140 pi <- items[1]
161 mu <- items[7:12] 161 mu <- items[7:12]
162 var <- items[13:18] 162 var <- items[13:18]
163 } 163 }
164 164
165 # Plot the output. 165 # Plot the output.
166 plot_ks(opt$kaks_input, number_comp, specified_colors, opt$output, pi, mu, var) 166 plot_ks(opt$kaks_input, number_comp, component_colors, opt$output, pi, mu, var)