plotVarPart-methods: Violin plot of variance fractions

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

Violin plot of variance fractions

Description

Violin plot of variance fraction for each gene and each variable

Usage

## S4 method for signature 'DataFrame'
plotVarPart(
  obj,
  col = c(ggColorHue(base::ncol(obj) - 3), "grey85"),
  label.angle = 20,
  main = "",
  ylab = "",
  convertToPercent = TRUE,
  ncol = 3,
  ...
)

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
ncol	number of columns in the plot
...	additional arguments

Value

Violin plot showing variance fractions

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)

# Summarize variance fractions genome-wide for each cell type
plotVarPart(vp)

GabrielHoffman/dreamlet documentation built on Oct. 29, 2024, 4:04 a.m.