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1 #!/usr/bin/env Rscript
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2
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3 suppressPackageStartupMessages(library("optparse"))
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26
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4 suppressPackageStartupMessages(library("rjson"))
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5
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6 option_list <- list(
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7 make_option(c("-c", "--components_input"), action="store", dest="components_input", help="Ks significant components input dataset"),
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8 make_option(c("-k", "--kaks_input"), action="store", dest="kaks_input", help="KaKs analysis input dataset"),
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35
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9 make_option(c("-n", "--number_comp"), action="store", dest="number_comp", type="integer", help="Number of significant components in the Ks distribution"),
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9
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10 make_option(c("-o", "--output"), action="store", dest="output", help="Output dataset"),
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23
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11 make_option(c("-r", "--colors"), action="store", default=NA, help="List of component colors")
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12 )
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13
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14 parser <- OptionParser(usage="%prog [options] file", option_list=option_list)
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15 args <- parse_args(parser, positional_arguments=TRUE)
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16 opt <- args$options
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17
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32
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18 set_component_colors = function(colors, number_comp)
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19 {
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20 # Handle colors for components.
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21 if (is.na(colors))
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22 {
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23 # Randomly specify colors for components.
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24 specified_colors <- c('red', 'yellow', 'green', 'black', 'blue', 'darkorange')
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25 }
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26 else
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27 {
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28 # Handle selected colors for components.
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29 parser <- newJSONParser()
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30 parser$addData(colors)
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31 raw_colors <- parser$getObject()
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32 specified_colors <- c()
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33 for (raw_color in raw_colors)
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34 {
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35 specified_colors <- c(specified_colors, raw_color)
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36 }
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37 num_colors_specified = length(specified_colors)
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38 if (num_colors_specified < number_comp)
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39 {
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40 for (i in num_colors_specified:number_comp)
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41 {
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42 if (!any(specified_colors=='red'))
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43 {
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44 specified_colors <- c(specified_colors, 'red')
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45 }
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46 else if (!any(specified_colors=='yellow'))
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47 {
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48 specified_colors <- c(specified_colors, 'yellow')
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49 }
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50 else if (!any(specified_colors=='green'))
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51 {
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52 specified_colors <- c(specified_colors, 'green')
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53 }
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54 else if (!any(specified_colors=='black'))
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55 {
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56 specified_colors <- c(specified_colors, 'black')
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57 }
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58 else if (!any(specified_colors=='blue'))
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59 {
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60 specified_colors <- c(specified_colors, 'blue')
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61 }
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62 else
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63 {
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64 specified_colors <- c(specified_colors, 'darkorange')
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65 }
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66 }
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67 }
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68 }
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69 return(specified_colors)
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32
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70 }
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71
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72 get_pi_mu_var = function(components_data, number_comp)
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73 {
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74 # FixMe: enhance this to generically handle any integer value for number_comp.
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75 if (number_comp == 1)
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76 {
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77 pi <- c(components_data[1, 9])
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78 mu <- c(components_data[1, 7])
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79 var <- c(components_data[1, 8])
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80 }
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81 else if (number_comp == 2)
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82 {
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83 pi <- c(components_data[2, 9], components_data[3, 9])
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84 mu <- c(components_data[2, 7], components_data[3, 7])
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85 var <- c(components_data[2, 8], components_data[3, 8])
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86 }
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87 else if (number_comp == 3)
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88 {
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89 pi <- c(components_data[4, 9], components_data[5, 9], components_data[6, 9])
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90 mu <- c(components_data[4, 7], components_data[5, 7], components_data[6, 7])
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91 var <- c(components_data[4, 8], components_data[5, 8], components_data[6, 8])
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92 }
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93 else if (number_comp == 4)
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94 {
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95 pi <- c(components_data[7, 9], components_data[8, 9], components_data[9, 9], components_data[10, 9])
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96 mu <- c(components_data[7, 7], components_data[8, 7], components_data[9, 7], components_data[10, 7])
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97 var <- c(components_data[7, 8], components_data[8, 8], components_data[9, 8], components_data[10, 8])
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98 }
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99 else if (number_comp == 5)
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4
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100 {
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101 pi <- c(components_data[11, 9], components_data[12, 9], components_data[13, 9], components_data[14, 9], components_data[15, 9])
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102 mu <- c(components_data[11, 7], components_data[12, 7], components_data[13, 7], components_data[14, 7], components_data[15, 7])
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103 var <- c(components_data[11, 8], components_data[12, 8], components_data[13, 8], components_data[14, 8], components_data[15, 8])
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104 }
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105 else if (number_comp == 6)
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4
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106 {
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107 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])
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108 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])
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109 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])
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110 }
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111 results = c(pi, mu, var)
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112 return(results)
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113 }
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114
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115 plot_ks<-function(kaks_input, number_comp, specified_colors, output, pi, mu, var)
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116 {
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117 # Start PDF device driver to save charts to output.
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118 pdf(file=output, bg="white")
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119 kaks <- read.table(file=kaks_input, header=T)
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120 max_ks <- max(kaks$Ks, na.rm=TRUE)
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121 # Change bin width
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122 max_bin_range <- as.integer(max_ks / 0.05)
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123 bin <- 0.05 * seq(0, (max_bin_range + 1 ))
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124 kaks <- kaks[kaks$Ks<max_ks,]
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125 h.kst <- hist(kaks$Ks, breaks=bin, plot=F)
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126 nc <- h.kst$counts
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127 vx <- h.kst$mids
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128 ntot <- sum(nc)
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129 # Set margin for plot bottom, left top, right.
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130 par(mai=c(0.5, 0.5, 0, 0))
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131 # Plot dimension in inches.
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132 par(pin=c(3.0, 3.0))
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133 g <- calculate_fitted_density(pi, mu, var, max_ks)
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134 h <- ntot * 1.5 / sum(g)
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135 vx <- seq(1, 100) * (max_ks / 100)
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136 ymax <- max(nc)
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137 barplot(nc, space=0.25, offset=0, width=0.04, xlim=c(0, max_ks), ylim=c(0, ymax), col="lightpink1", border="lightpink3")
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138 # Add x-axis.
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139 axis(1)
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140 for (i in 1:length(mu))
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141 {
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142 lines(vx, g[,i] * h, lwd=2, col=specified_colors[i])
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143 }
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144 }
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145
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146 calculate_fitted_density <- function(pi, mu, var, max_ks)
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147 {
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148 comp <- length(pi)
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149 var <- var/mu^2
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150 mu <- log(mu)
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151 # Calculate lognormal density.
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152 vx <- seq(1, 100) * (max_ks / 100)
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153 fx <- matrix(0, 100, comp)
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154 for (i in 1:100)
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155 {
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156 for (j in 1:comp)
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157 {
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158 fx[i, j] <- pi[j] * dlnorm(vx[i], meanlog=mu[j], sdlog=(sqrt(var[j])))
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159 if (is.nan(fx[i,j]))
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160 {
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161 fx[i,j]<-0
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162 }
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4
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163 }
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164 }
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165 return(fx)
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166 }
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167
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168 # Read in the components data.
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169 components_data <- read.delim(opt$components_input, header=TRUE)
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170 number_comp <- opt$number_comp
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171
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172 # Set component colors.
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173 specified_colors = set_component_colors(opt$colors, number_comp)
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174
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175 # Set pi, mu, var.
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176 items <- get_pi_mu_var(components_data, number_comp)
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177 if (number_comp == 1)
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178 {
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179 pi <- items[1]
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180 mu <- items[2]
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181 var <- items[3]
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182 }
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183 else if (number_comp == 2)
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184 {
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185 pi <- items[1:2]
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186 mu <- items[3:4]
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187 var <- items[5:6]
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188 }
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189 else if (number_comp == 3)
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190 {
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191 pi <- items[1:3]
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192 mu <- items[4:6]
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193 var <- items[7:9]
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194 }
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195 else if (number_comp == 4)
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196 {
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197 pi <- items[1:4]
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198 mu <- items[5:8]
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199 var <- items[9:12]
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200 }
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201 else if (number_comp == 5)
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202 {
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203 pi <- items[1:5]
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204 mu <- items[6:10]
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205 var <- items[11:15]
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206 }
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207 else if (number_comp == 6)
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208 {
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209 pi <- items[1:6]
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210 mu <- items[7:12]
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211 var <- items[13:18]
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212 }
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213
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214 # Plot the output.
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215 plot_ks(opt$kaks_input, number_comp, specified_colors, opt$output, pi, mu, var)
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