comparison ks_distribution.R @ 60:ae25785e78e1 draft

Uploaded

59:c5fb4e2ed4e2

option_list <- list(
    make_option(c("-c", "--components_input"), action="store", dest="components_input", help="Ks significant components input dataset"),
    make_option(c("-k", "--kaks_input"), action="store", dest="kaks_input", help="KaKs analysis input dataset"),
    make_option(c("-n", "--number_comp"), action="store", dest="number_comp", type="integer", help="Number of significant components in the Ks distribution"),
    make_option(c("-o", "--output"), action="store", dest="output", help="Output dataset"),
    make_option(c("-r", "--colors"), action="store", dest="colors", default=NA, help="List of component colors")
)

parser <- OptionParser(usage="%prog [options] file", option_list=option_list)
args <- parse_args(parser, positional_arguments=TRUE)
opt <- args$options

set_component_colors = function(colors, number_comp)
{
    # Handle colors for components.
    if (is.na(colors) == 0) {
        # Randomly specify colors for components.
        component_colors <- c('red', 'yellow', 'green', 'black', 'blue', 'darkorange')
    } else {
        # Handle selected colors for components.
        component_colors <- c()

    return(component_colors)
}

get_pi_mu_var = function(components_data, number_comp)
{
    # FixMe: enhance this to generically handle any integer value for number_comp.
    if (number_comp == 1) {
        pi <- c(components_data[1, 9])
        mu <- c(components_data[1, 7])
        var <- c(components_data[1, 8])
    } else if (number_comp == 2) {

# Read in the components data.
components_data <- read.delim(opt$components_input, header=TRUE)
number_comp <- as.integer(opt$number_comp)

# Set component colors.
component_colors <- set_component_colors(opt$colors, number_comp)

# Set pi, mu, var.
items <- get_pi_mu_var(components_data, number_comp)
if (number_comp == 1) {
	pi <- items[1]

60:ae25785e78e1

option_list <- list(
    make_option(c("-c", "--components_input"), action="store", dest="components_input", help="Ks significant components input dataset"),
    make_option(c("-k", "--kaks_input"), action="store", dest="kaks_input", help="KaKs analysis input dataset"),
    make_option(c("-n", "--number_comp"), action="store", dest="number_comp", type="integer", help="Number of significant components in the Ks distribution"),
    make_option(c("-o", "--output"), action="store", dest="output", help="Output dataset"),
    make_option(c("-s", "--specified_colors"), action="store", dest="specified_colors", default=NA, help="List of component colors")
)

parser <- OptionParser(usage="%prog [options] file", option_list=option_list)
args <- parse_args(parser, positional_arguments=TRUE)
opt <- args$options

set_component_colors = function(colors, number_comp)
{
    # Handle colors for components.
    if (is.na(colors)) {
        # Randomly specify colors for components.
        component_colors <- c('red', 'yellow', 'green', 'black', 'blue', 'darkorange')
    } else {
        # Handle selected colors for components.
        component_colors <- c()

    return(component_colors)
}

get_pi_mu_var = function(components_data, number_comp)
{
    if (number_comp == 1) {
        pi <- c(components_data[1, 9])
        mu <- c(components_data[1, 7])
        var <- c(components_data[1, 8])
    } else if (number_comp == 2) {

# Read in the components data.
components_data <- read.delim(opt$components_input, header=TRUE)
number_comp <- as.integer(opt$number_comp)

# Set component colors.
component_colors <- set_component_colors(opt$specified_colors, number_comp)

# Set pi, mu, var.
items <- get_pi_mu_var(components_data, number_comp)
if (number_comp == 1) {
	pi <- items[1]