plotPercentBars {variancePartition}R Documentation

Bar plot of variance fractions

Description

Bar plot of variance fractions for a subset of genes

Usage

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

Arguments

varPart

object returned by extractVarPart() or fitExtractVarPartModel()

col

color of bars for each variable

width

specify width of bars

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") 


[Package variancePartition version 1.23.3 Index]