atomizeSets: A function to make a mosaic-style plot for sets and their...

In leekgroup/Set: Decision-theoretic approach to gene-set analysis

Description

This function allows you to input a list of sets of features and visualize their atoms via a mosaic-style plot.

Usage

atomizeSets(sets, values = NULL, col = "red", bgCol = "ivory3",
  orderBy = "none", setLab = NULL, atomAvLab = NULL, ylab = "Atom size")

Arguments

sets	List representing sets of features.
values	Optional non-negative value (or weight) assigned to each feature. In the case that it is NULL, all features have the same weight.
col	Color representing sets and their respective atoms.
bgCol	Background color.
orderBy	If equal to "size", atoms are ordered by their sizes; if equal to "mean", atoms are ordered by the mean values assigned to their features.
setLab	Vector of set labels; if NULL, use the names of the sets list.
atomAvLab	Character representing labels above atoms in case the "mean" option is used in orderBy above; if NULL, use "Average in atom".
ylab	Character representing y-axis label.

Examples

sets <- list(A=1:50, B=31:130, C=131:160, D=c(40:50, 161:260))
atomizeSets(sets)

leekgroup/Set documentation built on May 20, 2019, 11:30 p.m.