comparison ks_distribution.R @ 32:4c3fcfd55d94 draft

Uploaded

31:812f09b96a62

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

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

plot_ks<-function(kaks_input, number_comp, 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 (length(colors) == 0))
    {
        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 < number_comp)
        {
            for (i in num_colors_specified:number_comp)
            {
                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])
    }
}

calculate_fitted_density <- function(pi, mu, var, max_ks)
{

        }
     }
    return(fx)
}

# Handle colors for components.
if (is.na(opt$colors))
{
    # Randomly specify colors for components.
    specified_colors <- c('red', 'yellow', 'green', 'black', 'blue', 'darkorange')
}
else
{
    # Handle selected colors for components.
    parser <- newJSONParser()
    parser$addData(opt$colors)
    raw_colors <- parser$getObject()
    specified_colors <- c()
    for (raw_color in raw_colors)
    {
        specified_colors <- c(specified_colors, raw_color)
    }
}

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

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

32:4c3fcfd55d94

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.
        specified_colors <- c('red', 'yellow', 'green', 'black', 'blue', 'darkorange')
    }
    else
    {
        # Handle selected colors for components.
        parser <- newJSONParser()
        parser$addData(colors)
        raw_colors <- parser$getObject()
        specified_colors <- c()
        for (raw_color in raw_colors)
        {
            specified_colors <- c(specified_colors, raw_color)
        }
        num_colors_specified = length(specified_colors)
        if (num_colors_specified < number_comp)
        {
            for (i in num_colors_specified:number_comp)
            {
                if (!any(specified_colors=='red'))
                {
                    specified_colors <- c(specified_colors, 'red')
                }
                else if (!any(specified_colors=='yellow'))
                {
                    specified_colors <- c(specified_colors, 'yellow')
                }
                else if (!any(specified_colors=='green'))
                {
                    specified_colors <- c(specified_colors, 'green')
                }
                else if (!any(specified_colors=='black'))
                {
                    specified_colors <- c(specified_colors, 'black')
                }
                else if (!any(specified_colors=='blue'))
                {
                    specified_colors <- c(specified_colors, 'blue')
                }
                else
                {
                    specified_colors <- c(specified_colors, 'darkorange')
                }
            }
        }
    }
    return specified_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)
    {

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

plot_ks<-function(kaks_input, number_comp, specified_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)
    for (i in 1:length(mu))
    {
       lines(vx, g[,i] * h, lwd=2, col=specified_colors[i])
    }
}

calculate_fitted_density <- function(pi, mu, var, max_ks)
{

        }
     }
    return(fx)
}

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

# Set component colors.
specified_colors = set_component_colors = function(opt$colors, number_comp)

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