plotAnnoScoreDist: Plot ranked region set scores, annotating groups of interest

In COCOA: Coordinate Covariation Analysis

Description

Visualize the distribution of region set scores for region set groups of interest.

Usage

plotAnnoScoreDist(
  rsScores,
  colToPlot,
  pattern,
  patternName = pattern,
  rsNameCol = "rsName",
  alpha = 0.5,
  shape = 3
)

Arguments

rsScores	data.frame. Each row should be a region set. Columns should include score columns and a column that contains the name of each region set.
colToPlot	character. Name of the column with region set scores to plot.
pattern	character. Region sets that match each pattern will be given the same color. Multiple patterns can be given as character objects in a vector (each will have a different color). Regular expressions can be used (ignore.case=TRUE though). For example, to search for ER or GATA3 and color with a single color, this pattern can be given "ER|GATA3".
patternName	character. A name for each string in "pattern" that will be used for the legend.
rsNameCol	character. Column name of "rsScores" column that contains the name or description of each region set. This column will be searched for the pattern given by the "pattern" parameter.
alpha	numeric. Transparency of points. See ggplot documentation for further details.
shape	integer. Shape of the points. See ggplot documentation for options.

Details

If the same region set matches two patterns, the later group will be assigned to that region set.

Value

ggplot object that can be modified using ggplot syntax. E.g. plot + ggplot_function

Examples

data(rsScores)
rsScores$rsName <- c("ER", "GATA3", "ER", "GATA3", "AP1") 
plotAnnoScoreDist(rsScores, colToPlot="PC1", pattern="ER", alpha=1)
plotAnnoScoreDist(rsScores, colToPlot="PC2", pattern=c("ER", "GATA3"))

COCOA documentation built on Nov. 8, 2020, 5:42 p.m.