Plot Gene Expression Violin Plots Stratified by Group

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

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)

Value

p a ggplot object

Details

Generates a 2d plot of cells with gene expression

See also

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