Cleaned up old visualization files

radseq_analysis/visualization/r_plots.py

-import os
-
-
-def frequencies(file, output_dir):
-
-    scripts_d = ''.join(os.path.split(os.path.realpath(__file__))[:-1])
-    cmd = ('Rscript ' + os.path.join(scripts_d, 'r_scripts', 'frequencies.R') +
-           ' ' + file + ' ' + output_dir)
-    os.system(cmd)
-
-
-def haplotypes(file, output_dir, threshold):
-
-    scripts_d = ''.join(os.path.split(os.path.realpath(__file__))[:-1])
-    cmd = ('Rscript ' + os.path.join(scripts_d, 'r_scripts', 'haplotypes.R') +
-           ' ' + file + ' ' + output_dir + ' ' + str(threshold))
-    os.system(cmd)

radseq_analysis/visualization/r_scripts/haplotypes.R

-#!/usr/bin/env Rscript
-args = commandArgs(trailingOnly=TRUE)
-
-# test if there is at least one argument: if not, return an error
-if (length(args)==0) {
-    stop("At least one argument must be supplied (input file).n", call.=FALSE)
-} else if (length(args) != 3){
-    stop("Usage: R haplotypes.R input_file.tsv output_dir treshold")
-}
-
-suppressMessages(library(readr))
-suppressMessages(library(ggplot2))
-suppressMessages(library(gridExtra))
-
-file = args[1]
-output_dir = args[2]
-threshold = args[3]
-
-png_name = paste("sex_variable_haplotypes.png", sep='')
-
-data <- suppressMessages(read_delim(file, "\t", col_names = TRUE, escape_double = FALSE, trim_ws = TRUE))
-names(data) = c('Locus', 'Male_haplotype', 'Male_haplotype_number',
-                'Female_haplotype', 'Female_haplotype_number',
-                'Males', 'Females', 'Male_outliers',
-                'Female_outliers', 'Consensus')
-
-males = data.frame(table(data$Male_haplotype_number[which(data$Male_haplotype_number > threshold)], data$Female_haplotype_number[which(data$Male_haplotype_number > threshold)]))
-names(males) = c('Males', 'Females', 'Count')
-
-females = data.frame(table(data$Male_haplotype_number[which(data$Female_haplotype_number > threshold)], data$Female_haplotype_number[which(data$Female_haplotype_number > threshold)]))
-names(females) = c('Males', 'Females', 'Count')
-
-g <- ggplot(males, aes(x = Males, y = Count, fill = Females))
-g = g + geom_bar(stat='identity', position=position_dodge(), colour='black')
-
-h <- ggplot(females, aes(x = Females, y = Count, fill = Males))
-h = h + geom_bar(stat='identity', position=position_dodge(), colour='black')
-
-png(paste(output_dir, png_name, sep=''), width=1600, height=1000, res=130)
-grid.arrange(g, h, ncol=2)
-x = dev.off()
-

radseq_analysis/visualization/visualisation.py

-import os
-from . import r_plots
-
-
-def run(global_parameters):
-
-    results_dir = os.path.join(global_parameters.results_dir, '')
-    print(' - Plotting frequencies data')
-    r_plots.frequencies(global_parameters.frequencies_file, results_dir)
-    print(' - Plotting haplotypes data')
-    r_plots.haplotypes(global_parameters.haplotypes_file, results_dir, global_parameters.error_threshold)