plotPercentBars {variancePartition}R Documentation

Bar plot of gene fractions

Description

Bar plot of fractions for a subset of genes

Usage

plotPercentBars(
  x,
  col = c(ggColorHue(ncol(x) - 1), "grey85"),
  genes = rownames(x),
  width = NULL
)

## S4 method for signature 'matrix'
plotPercentBars(
  x,
  col = c(ggColorHue(ncol(x) - 1), "grey85"),
  genes = rownames(x),
  width = NULL
)

## S4 method for signature 'data.frame'
plotPercentBars(
  x,
  col = c(ggColorHue(ncol(x) - 1), "grey85"),
  genes = rownames(x),
  width = NULL
)

## S4 method for signature 'varPartResults'
plotPercentBars(
  x,
  col = c(ggColorHue(ncol(x) - 1), "grey85"),
  genes = rownames(x),
  width = NULL
)

Arguments

x

object storing fractions

col

color of bars for each variable

genes

name of genes to plot

width

specify width of bars

Value

Returns ggplot2 barplot

Examples

# library(variancePartition)

library(BiocParallel)

# 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 1.24.1 Index]