plotViolin-methods: Plot Violins

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

Plot Violins

Description

Plot Violins

Usage

plotViolin(x, ...)

## S4 method for signature 'cellSpecificityValues'
plotViolin(x, assays = colnames(x))

Arguments

x	fractions for each gene
...	other arguments
assays	array of assays to plot

Value

Violin plot

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
)

# Compute cell type specificity of each gene
df <- cellTypeSpecificity(pb)

# Violin plot of specificity scores for each cell type
# Dashed line indicates genes that are equally expressed
# across all cell types.  For K cell types, this is 1/K
plotViolin(df)

GabrielHoffman/dreamlet documentation built on May 20, 2024, 2:05 p.m.