Mercurial > repos > greg > ks_distribution
changeset 60:ae25785e78e1 draft
Uploaded
| author | greg |
|---|---|
| date | Tue, 27 Jun 2017 08:06:19 -0400 |
| parents | c5fb4e2ed4e2 |
| children | c19c48db9f79 |
| files | ks_distribution.R |
| diffstat | 1 files changed, 3 insertions(+), 4 deletions(-) [+] |
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--- a/ks_distribution.R Tue Jun 27 08:06:10 2017 -0400 +++ b/ks_distribution.R Tue Jun 27 08:06:19 2017 -0400 @@ -7,7 +7,7 @@ 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") + 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) @@ -17,7 +17,7 @@ set_component_colors = function(colors, number_comp) { # Handle colors for components. - if (is.na(colors) == 0) { + if (is.na(colors)) { # Randomly specify colors for components. component_colors <- c('red', 'yellow', 'green', 'black', 'blue', 'darkorange') } else { @@ -52,7 +52,6 @@ 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]) @@ -136,7 +135,7 @@ number_comp <- as.integer(opt$number_comp) # Set component colors. -component_colors <- set_component_colors(opt$colors, number_comp) +component_colors <- set_component_colors(opt$specified_colors, number_comp) # Set pi, mu, var. items <- get_pi_mu_var(components_data, number_comp)