comparison ks_distribution.R @ 9:214e2710c51e draft

Uploaded

8:1650842a90ba

suppressPackageStartupMessages(library("optparse"))

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("-o", "--output"), action="store", dest="output", help="Output dataset")
)

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


get_num_components = function(components_data)
{
    # Get the max of the number_comp column.
    number_comp = components_data[, 3]
    num_components <- max(number_comp, na.rm=TRUE)
    return(num_components)
}

get_pi_mu_var = function(components_data, num_components)
{
    # FixMe: enhance this to generically handle any integer value for num_components.
    if (num_components == 1)

    }
    results = c(pi, mu, var)
    return(results)
}

plot_ks<-function(kaks_input, output, pi, mu, var)
{
    # Start PDF device driver to save charts to output.
    pdf(file=output, bg="white")
    kaks <- read.table(file=kaks_input, header=T)
    max_ks <- max(kaks$Ks, na.rm=TRUE)

    vx <- seq(1, 100) * (max_ks / 100)
    ymax <- max(nc)
    barplot(nc, space=0.25, offset=0, width=0.04, xlim=c(0, max_ks), ylim=c(0, ymax), col="lightpink1", border="lightpink3")
    # Add x-axis.
    axis(1)
    color <- c('red', 'yellow','green','black','blue', 'darkorange' )
    for (i in 1:length(mu))
    {
       lines(vx, g[,i] * h, lwd=2, col=color[i])
    }
}

    return(fx)
}

# Read in the components data.
components_data <- read.delim(opt$components_input, header=TRUE)
# Get the number of components.
num_components <- get_num_components(components_data)

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

	mu <- items[7:12]
	var <- items[13:18]
}

# Plot the output.
plot_ks(opt$kaks_input, opt$output, pi, mu, var)

9:214e2710c51e

suppressPackageStartupMessages(library("optparse"))

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", "--num_comp"), action="store", dest="num_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", 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

get_pi_mu_var = function(components_data, num_components)
{
    # FixMe: enhance this to generically handle any integer value for num_components.
    if (num_components == 1)

    }
    results = c(pi, mu, var)
    return(results)
}

plot_ks<-function(kaks_input, num_components, colors, output, pi, mu, var)
{
    # Start PDF device driver to save charts to output.
    pdf(file=output, bg="white")
    kaks <- read.table(file=kaks_input, header=T)
    max_ks <- max(kaks$Ks, na.rm=TRUE)

    vx <- seq(1, 100) * (max_ks / 100)
    ymax <- max(nc)
    barplot(nc, space=0.25, offset=0, width=0.04, xlim=c(0, max_ks), ylim=c(0, ymax), col="lightpink1", border="lightpink3")
    # Add x-axis.
    axis(1)
    if(is.na(colors)
    {
        color <- c('red', 'yellow', 'green', 'black', 'blue', 'darkorange')
    }
    else
    {
        # Handle specified colors for components.
        cStr <- unlist(colors)
        color <- c()
        items <- strsplit(cStr, ",")
        for (item in items) {
            color <- c(color, item)
        }
        num_colors_specified = length(color)
        if num_colors_specified < num_components:
        {
            for (i in num_colors_specified:num_components)
            {
                if !(any(color=='red')
                {
                    color <- c(color, 'red')
                }
                else if !(any(color=='yellow')
                {
                    color <- c(color, 'yellow')
                }
                else if !(any(color=='green')
                {
                    color <- c(color, 'green')
                }
                else if !(any(color=='black')
                {
                    color <- c(color, 'black')
                }
                else if !(any(color=='blue')
                {
                    color <- c(color, 'blue')
                }
                else
                {
                    color <- c(color, 'darkorange')
                }
            }
        }
    }
    for (i in 1:length(mu))
    {
       lines(vx, g[,i] * h, lwd=2, col=color[i])
    }
}

    return(fx)
}

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

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

	mu <- items[7:12]
	var <- items[13:18]
}

# Plot the output.
plot_ks(opt$kaks_input, num_components, opt$colors, opt$output, pi, mu, var)