plotPvalplot: Plot results from unidirectional enrichment

In saeyslab/triwise: Gene expression changes in three biological conditions

Description

Plots each enriched gene set as a dot on a dotplot

Usage

plotPvalplot(scores, Coi = c("", "", ""), colorby = NULL,
  showlabels = TRUE, baseangle = 0)

Arguments

scores	Dataframe as returned by testUnidirectionality containing for every gene set a q-value and an associated angle
Coi	Names of the three biological conditions, only used for labelling
colorby	Column in 'scores' used for coloring
showlabels	Whether to show labels on the grid
baseangle	The angle by which to rotate the whole plot (default to '0')

Value

A ggplot2 plot, which can be used for further customization

Examples

Eoi = matrix(rnorm(1000*3, sd=0.5), 1000, 3, dimnames=list(1:1000, c(1,2,3)))
Eoi[1:100,1] = Eoi[1:100,1] + 4 # the first 100 genes are more upregulated in the first condition
barycoords = transformBarycentric(Eoi)

gsets = list(a=1:50, b=80:150, c=200:500)
scores = testUnidirectionality(barycoords, gsets, Gdiffexp=(1:1000)[barycoords$r > 1])

plotPvalplot(scores)

saeyslab/triwise documentation built on May 29, 2019, 12:56 p.m.