plotPercentBars-method: Bar plot of gene fractions

In GabrielHoffman/variancePartition: Quantify and interpret drivers of variation in multilevel gene expression experiments

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
...	other arguments

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")

GabrielHoffman/variancePartition documentation built on Nov. 8, 2024, 11:17 a.m.