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"))

### Arguments

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

### Value

Returns ggplot2 barplot

### Examples

    # library(variancePartition)

    # optional step to run analysis in parallel on multicore machines
    # Here, we used 4 threads
    library(doParallel)
    cl <- makeCluster(4)
    registerDoParallel(cl)
    # or by using the doSNOW package

    # 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")

    # stop cluster
    stopCluster(cl)

[Package variancePartition version 1.12.3 Index]