plotPercentBars-methods: Bar plot of variance fractions

In GabrielHoffman/dreamlet: Scalable differential expression analysis of single cell transcriptomics datasets with complex study designs

Bar plot of variance fractions

Description

Bar plot of variance fractions for a subset of genes

Usage

## S4 method for signature 'vpDF'
plotPercentBars(
  x,
  col = c(ggColorHue(ncol(x) - 3), "grey85"),
  genes = unique(x$gene),
  width = NULL,
  ncol = 3,
  ...
)

## S4 method for signature 'cellSpecificityValues'
plotPercentBars(
  x,
  col = ggColorHue(ncol(x)),
  genes = rownames(x),
  width = NULL,
  ...
)

Arguments

x	vpDF object returned by fitVarPart()
col	color of bars for each variable
genes	name of genes to plot
width	specify width of bars
ncol	number of columns in the plot
...	other arguments

Value

Bar plot showing variance fractions for each gene

Examples

library(muscat)
library(SingleCellExperiment)

data(example_sce)

# create pseudobulk for each sample and cell cluster
pb <- aggregateToPseudoBulk(example_sce,
  assay = "counts",
  cluster_id = "cluster_id",
  sample_id = "sample_id",
  verbose = FALSE
)

# voom-style normalization
res.proc <- processAssays(pb, ~group_id)

# variance partitioning analysis
vp <- fitVarPart(res.proc, ~group_id)

# Show variance fractions at the gene-level for each cell type
plotPercentBars(vp, genes = vp$gene[2:4], ncol = 2)

GabrielHoffman/dreamlet documentation built on Nov. 23, 2024, 12:28 a.m.