plot_sex_distribution: Plot sex distribution

In RomainFeron/radsex-vis: Visualization of results from the RADSex pipeline

Description

Plots a heatmap of distribution of sequences between sexes from a table generated with RADSex distrib

Usage

plot_sex_distribution(input_file_path, output_file_path = NULL,
  title = NULL, width = 8, height = 7, dpi = 300,
  autoscale = FALSE, show.significance = TRUE,
  significance.color = "red3", significance.threshold = 0.05,
  color.scale.bins = c(0, 1, 5, 25, 100, 1000),
  color.scale.colors = c("white", "navyblue"))

Arguments

input_file_path	Path to a table of distribution of sequences between sexes.
output_file_path	Path to the plot output file. If no output file is specified, the heatmap will be plotted in the default device (default NULL).
title	Plot title (default NULL).
width	Width of the output file in inches (default 8).
height	Height of the output file in inches (default 7).
dpi	Resolution of the output file (default 300).
autoscale	If set to TRUE, the height of the output file will be automatically set so that horizontal and vertical scales are equal. The resulting heatmap will not be square if the number of males and females in the population are very different (default FALSE).
show.significance	If TRUE, tiles with significant association with sex are highlighted with the color defined in the significance.color parameter (default TRUE).
significance.color	Color of the border for tiles significantly associated with sex (default "red3").
significance.threshold	P-value threshold to consider a tile significantly associated with sex (default 0.05).
color.scale.bins	A vector of values to use as bins in the color palette (default c(0, 1, 5, 25, 100, 1000)).
color.scale.colors	A vector of two colors used to create the color palette gradient (default c("white", "navyblue")).

Examples

# No autoscale: the plot dimensions are specified with "width" and "height".
plot_sex_distribution("sex_distribution_table.tsv", output_file_path = "heatmap.png",
                      title = "Distribution of sequences between sexes",
                      width = 10, height = 10, dpi = 200,
                      significance.color = "gold", significance.threshold = 0.05,
                      color.scale.bins = c(0, 10, 100, 1000),
                      color.scale.colors = c("white", "grey10"))

# Autoscale: the plot dimensions are automatically calculated from "width".
plot_sex_distribution("sex_distribution_table.tsv", output_file_path = "heatmap.png",
                      title = "Distribution of sequences between sexes",
                      width = 10, autoscale = TRUE)

RomainFeron/radsex-vis documentation built on May 23, 2019, 2:48 p.m.