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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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4
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5 option_list <- list(
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6 make_option(c("-c", "--components_input"), action="store", dest="components_input", help="Ks significant components input dataset"),
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7 make_option(c("-k", "--kaks_input"), action="store", dest="kaks_input", help="KaKs analysis input dataset"),
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8 make_option(c("-o", "--output"), action="store", dest="output", help="Output dataset")
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9 )
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10
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11 parser <- OptionParser(usage="%prog [options] file", option_list=option_list)
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12 args <- parse_args(parser, positional_arguments=TRUE)
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13 opt <- args$options
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14
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15
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16 get_num_components = function(components_data)
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17 {
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18 # Get the max of the number_comp column.
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19 number_comp = components_data[, 3]
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20 num_components <- max(number_comp, na.rm=TRUE)
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21 return(num_components)
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22 }
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23
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24 get_pi_mu_var = function(components_data, num_components)
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25 {
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26 # FixMe: enhance this to generically handle any integer value for num_components.
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27 if (num_components == 1)
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28 {
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4
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29 pi <- c(components_data[1, 9])
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30 mu <- c(components_data[1, 7])
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31 var <- c(components_data[1, 8])
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32 }
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33 else if (num_components == 2)
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34 {
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35 pi <- c(components_data[2, 9], components_data[3, 9])
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36 mu <- c(components_data[2, 7], components_data[3, 7])
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37 var <- c(components_data[2, 8], components_data[3, 8])
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38 }
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39 else if (num_components == 3)
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40 {
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41 pi <- c(components_data[4, 9], components_data[5, 9], components_data[6, 9])
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42 mu <- c(components_data[4, 7], components_data[5, 7], components_data[6, 7])
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43 var <- c(components_data[4, 8], components_data[5, 8], components_data[6, 8])
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44 }
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45 else if (num_components == 4)
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46 {
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47 pi <- c(components_data[7, 9], components_data[8, 9], components_data[9, 9], components_data[10, 9])
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48 mu <- c(components_data[7, 7], components_data[8, 7], components_data[9, 7], components_data[10, 7])
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49 var <- c(components_data[7, 8], components_data[8, 8], components_data[9, 8], components_data[10, 8])
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50 }
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51 else if (num_components == 5)
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52 {
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53 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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54 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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55 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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56 }
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57 else if (num_components == 6)
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58 {
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59 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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60 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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61 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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62 }
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63 results = c(pi, mu, var)
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64 return(results)
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65 }
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66
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67 plot_ks<-function(kaks_input, output, pi, mu, var)
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68 {
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69 # Start PDF device driver to save charts to output.
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70 pdf(file=output, bg="white")
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4
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71 kaks <- read.table(file=kaks_input, header=T)
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72 max_ks <- max(kaks$Ks, na.rm=TRUE)
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73 # Change bin width
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74 max_bin_range <- as.integer(max_ks / 0.05)
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75 bin <- 0.05 * seq(0, (max_bin_range + 1 ))
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76 kaks <- kaks[kaks$Ks<max_ks,]
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77 h.kst <- hist(kaks$Ks, breaks=bin, plot=F)
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78 nc <- h.kst$counts
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79 vx <- h.kst$mids
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80 ntot <- sum(nc)
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81 # Set margin for plot bottom, left top, right.
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82 par(mai=c(0.5, 0.5, 0, 0))
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83 # Plot dimension in inches.
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84 par(pin=c(3.0, 3.0))
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85 g <- calculate_fitted_density(pi, mu, var, max_ks)
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86 h <- ntot * 1.5 / sum(g)
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87 vx <- seq(1, 100) * (max_ks / 100)
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88 ymax <- max(nc)
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89 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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90 # Add x-axis.
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91 axis(1)
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92 color <- c('red', 'yellow','green','black','blue', 'darkorange' )
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93 for (i in 1:length(mu))
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94 {
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95 lines(vx, g[,i] * h, lwd=2, col=color[i])
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96 }
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97 }
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98
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99 calculate_fitted_density <- function(pi, mu, var, max_ks)
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100 {
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101 comp <- length(pi)
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102 var <- var/mu^2
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103 mu <- log(mu)
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104 # Calculate lognormal density.
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105 vx <- seq(1, 100) * (max_ks / 100)
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106 fx <- matrix(0, 100, comp)
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107 for (i in 1:100)
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108 {
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109 for (j in 1:comp)
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110 {
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111 fx[i, j] <- pi[j] * dlnorm(vx[i], meanlog=mu[j], sdlog=(sqrt(var[j])))
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112 if (is.nan(fx[i,j])) fx[i,j]<-0
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113 }
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114 }
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115 return(fx)
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116 }
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117
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118 # Read in the components data.
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119 components_data <- read.delim(opt$components_input, header=TRUE)
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120 # Get the number of components.
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121 num_components <- get_num_components(components_data)
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122
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123 # Set pi, mu, var.
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124 items <- get_pi_mu_var(components_data, num_components)
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125 if (num_components == 1)
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126 {
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127 pi <- items[1]
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128 mu <- items[2]
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129 var <- items[3]
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130 }
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131 if (num_components == 2)
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132 {
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133 pi <- items[1:2]
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134 mu <- items[3:4]
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135 var <- items[5:6]
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136 }
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137 if (num_components == 3)
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138 {
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139 pi <- items[1:3]
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140 mu <- items[4:6]
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141 var <- items[7:9]
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142 }
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143 if (num_components == 4)
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144 {
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145 pi <- items[1:4]
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146 mu <- items[5:8]
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147 var <- items[9:12]
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148 }
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149 if (num_components == 5)
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150 {
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151 pi <- items[1:5]
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152 mu <- items[6:10]
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153 var <- items[11:15]
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154 }
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155 if (num_components == 6)
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156 {
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157 pi <- items[1:6]
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158 mu <- items[7:12]
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159 var <- items[13:18]
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160 }
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161
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162 # Plot the output.
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163 plot_ks(opt$kaks_input, opt$output, pi, mu, var)
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