plotPercentBars {variancePartition} | R Documentation |
Bar plot of variance fractions for a subset of genes
plotPercentBars(varPart, col = c(ggColorHue(ncol(varPart) - 1), "grey85"))
varPart |
object returned by extractVarPart() or fitExtractVarPartModel() |
col |
color of bars for each variable |
Returns ggplot2 barplot
# 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)