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