plotPercentBars: Bar plot of variance fractions

In variancePartition: Quantify and interpret divers of variation in multilevel gene expression experiments

Description

Bar plot of variance fractions for a subset of genes

Usage

plotPercentBars(varPart, col = c(ggColorHue(ncol(varPart) - 1), "grey85"))

Arguments

varPart	object returned by extractVarPart() or fitExtractVarPartModel()
col	color of bars for each variable

Value

Returns ggplot2 barplot

Examples

# library(variancePartition)

# Intialize parallel backend with 4 cores
library(BiocParallel)
register(SnowParam(4))

# load simulated data:
# geneExpr: matrix of gene expression values
# info: information/metadata about each sample
data(varPartData)

# Specify variables to consider
form <- ~ Age + (1|Individual) + (1|Tissue)

# Fit model
varPart <- fitExtractVarPartModel( geneExpr, form, info )

# Bar plot for a subset of genes showing variance fractions
plotPercentBars( varPart[1:5,] )

# Move the legend to the top
plotPercentBars( varPart[1:5,] ) + theme(legend.position="top") 

variancePartition documentation built on Nov. 8, 2020, 5:18 p.m.