Mercurial > repos > greg > kaks_analysis_barplot

comparison kaks_analysis_barplot.R @ 0:844acb833219 draft

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author greg
date Wed, 08 Mar 2017 08:55:19 -0500
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children b4f599423810
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-1:000000000000 0:844acb833219
1 #!/usr/bin/env Rscript
2
3 suppressPackageStartupMessages(library("optparse"))
4
5 option_list <- list(
6 make_option(c("-c", "--components"), action="store", dest="components", help="Ks significant components input dataset"),
7 make_option(c("-o", "--output"), action="store", dest="output", default=NULL, help="Output dataset"),
8 )
9
10 parser <- OptionParser(usage="%prog [options] file", option_list=option_list)
11 args <- parse_args(parser, positional_arguments=TRUE)
12 opt <- args$options
13
14
15 get_num_components=function(components_dataset)
16 {
17 # Read in the components data.
18 components_data <- read.delim(components_dataset, header=TRUE);
19 # Get the max of the number_comp column.
20 num_components <- max(components_data[3, ], na.rm=TRUE);
21 return = c(components_data, num_components)
22 return
23 }
24
25 get_pi_mu_var = function(components_data, num_components) {
26 # FixMe: enhance this to generically handle any integer value for num_components.
27 if (num_components == 1) {
28 pi <- c(components_data[1, 9]);
29 mu <- c(components_data[1, 7]);
30 var <- c(components_data[1, 8]);
31 } else if (num_components == 2) {
32 pi <- c(components_data[2, 9], components_data[3, 9]);
33 mu <- c(components_data[2, 7], components_data[3, 7]);
34 var <- c(components_data[2, 8], components_data[3, 8]);
35 } else if (num_components == 3) {
36 pi <- c(components_data[4, 9], components_data[5, 9], components_data[6, 9]);
37 mu <- c(components_data[4, 7], components_data[5, 7], components_data[6, 7]);
38 var <- c(components_data[4, 8], components_data[5, 8], components_data[6, 8]);
39 } else if (num_components == 4) {
40 pi <- c(components_data[7, 9], components_data[8, 9], components_data[9, 9], components_data[10, 9]);
41 mu <- c(components_data[7, 7], components_data[8, 7], components_data[9, 7], components_data[10, 7]);
42 var <- c(components_data[7, 8], components_data[8, 8], components_data[9, 8], components_data[10, 8]);
43 return = c(pi, mu, var)
44 return
45 }
46
47 plot_ks<-function(ksfile, pi, mu, var) {
48 #change bin width
49 bin <- 0.05 * seq(0, 40);
50 kaks <- read.table(file=ksfile, header=T);
51 kaks <- kaks[kaks$Ks<2,];
52 h.kst <- hist(kaks$Ks, breaks=bin, plot=F);
53 nc <- h.kst$counts;
54 vx <- h.kst$mids;
55 ntot <- sum(nc);
56 # Set margin for plot bottom, left top, right.
57 par(mai=c(0.5, 0.5, 0, 0));
58 # Plot dimension in inches.
59 par(pin=c(2.5, 2.5));
60 g <- calculate_fitted_density(pi, mu, var);
61 h <- ntot * 2.5 / sum(g);
62 vx <- seq(1, 100) * 0.02;
63 ymax <- max(nc) + 5;
64 barplot(nc, space=0.25, offset=0, width=0.04, xlim=c(0,2), ylim=c(0, ymax));
65 # Add x-axis.
66 axis(1);
67 color <- c('green', 'blue', 'black', 'red');
68 for (i in 1:length(mu)) {
69 lines(vx, g[,i] * h, lwd=2, col=color[i]);
70 }
71 };
72
73 calculate_fitted_density <- function(pi, mu, var) {
74 comp <- length(pi);
75 var <- var/mu^2;
76 mu <- log(mu);;
77 #calculate lognormal density
78 vx <- seq(1, 100) * 0.02;
79 fx <- matrix(0, 100, comp);
80 for (i in 1:100) {
81 for (j in 1:comp) {
82 fx[i, j] <- pi[j] * dlnorm(vx[i], meanlog=mu[j], sdlog=(sqrt(var[j])));
83 };
84 };
85 fx;
86 }
87
88 # Read in the components data and get the number of components.
89 items <- get_num_components(opt$components)
90 components_data <- items[1]
91 num_components <- items[2]
92
93 # Set output file name.
94 if (is.null(opt$output)) {
95 # Name the output file based on the name of the
96 # input file, properly handling full path if passed.
97 input_filename = basename(opt$components)
98 items = strsplit(input_filename, ".")
99 output_filename <- paste(items[1], ".components.", num_components, ".pdf")
100 } else {
101 output_filename <- opt$output
102 }
103
104 # Set pi, mu, var.
105 items <- get_pi_mu_var(components_data, num_components)
106 pi <- items[1]
107 mu <- items[2]
108 var <- items[3]
109
110 # Plot the output.
111 plot_ks(output_filename, pi, mu, var)