plotPvalplot: Plot results from unidirectional enrichment

Description Usage Arguments Value Examples

View source: R/visualize.R

Description

Plots each enriched gene set as a dot on a dotplot

Usage

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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

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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)

Zouter/triwise documentation built on June 3, 2017, 10:50 a.m.