plotVarPart-method: Violin plot of variance fractions

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

Description

Violin plot of variance fraction for each gene and each variable

Usage

plotVarPart(
  obj,
  col = c(ggColorHue(ncol(obj) - 1), "grey85"),
  label.angle = 20,
  main = "",
  ylab = "",
  convertToPercent = TRUE,
  ...
)

## S4 method for signature 'matrix'
plotVarPart(
  obj,
  col = c(ggColorHue(ncol(obj) - 1), "grey85"),
  label.angle = 20,
  main = "",
  ylab = "",
  convertToPercent = TRUE,
  ...
)

## S4 method for signature 'data.frame'
plotVarPart(
  obj,
  col = c(ggColorHue(ncol(obj) - 1), "grey85"),
  label.angle = 20,
  main = "",
  ylab = "",
  convertToPercent = TRUE,
  ...
)

## S4 method for signature 'varPartResults'
plotVarPart(
  obj,
  col = c(ggColorHue(ncol(obj) - 1), "grey85"),
  label.angle = 20,
  main = "",
  ylab = "",
  convertToPercent = TRUE,
  ...
)

Arguments

obj	varParFrac object returned by fitExtractVarPart or extractVarPart
col	vector of colors
label.angle	angle of labels on x-axis
main	title of plot
ylab	text on y-axis
convertToPercent	multiply fractions by 100 to convert to percent values
...	additional arguments

Value

Makes violin plots of variance components model. This function uses the graphics interface from ggplot2. Warnings produced by this function usually ggplot2 warning that the window is too small.

Examples

# load library
# 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
# Age is continuous so we model it as a fixed effect
# Individual and Tissue are both categorical, so we model them as random effects
form <- ~ Age + (1|Individual) + (1|Tissue) 

varPart <- fitExtractVarPartModel( geneExpr, form, info )
 
# violin plot of contribution of each variable to total variance
plotVarPart( sortCols( varPart ) )

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