plot_violin: Plot Gene Expression Violin Plots Stratified by Group

In combiz/scFlow: A Single-Cell/Nuclei Analysis Toolkit

Plot Gene Expression Violin Plots Stratified by Group

Description

Plots the cells in reduced dimensionality space with log10 expression values for a specified gene.

Usage

plot_violin(
  sce,
  group_var = "group",
  subset_var = "cluster_celltype",
  subset_group = "Oligo",
  gene = "PLP1",
  var_order = NULL,
  palette = NULL,
  alpha = 0.05,
  size = 0.01,
  label_angle = 0
)

Arguments

sce	a SingleCellExperiment object
group_var	The colData variable for x-axis groups
subset_var	The colData variable to subset on
subset_group	The specific subset_var group to subset
gene	The gene of interest
var_order	Optional re-ordering of subset_group factor levels
palette	Optional custom palette
alpha	point alpha
size	point size
label_angle	The angle of x-axis labels (e.g. 0, 45)

Details

Generates a 2d plot of cells with gene expression

Value

p a ggplot object

See Also

Other plotting functions: plot_expr_by_numeric_var(), plot_reduced_dim(), plot_reduced_dim_gene()

combiz/scFlow documentation built on Feb. 25, 2024, 10:25 a.m.