plot_reduced_dim_gene: Plot Cells Reduced Dimensions With Gene Expression

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

Plot Cells Reduced Dimensions With Gene Expression

Description

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

Usage

plot_reduced_dim_gene(
  sce,
  reduced_dim = "UMAP",
  gene = "PLP1",
  size = getOption("scflow_reddimplot_pointsize", default = 0.1),
  alpha = getOption("scflow_reddimplot_alpha", default = 0.2),
  palette = c("grey80", "#440154FF")
)

Arguments

sce	a SingleCellExperiment object
reduced_dim	the reducedDim slot for plotting
gene	the gene of interest
size	point size
alpha	point alpha
palette	off and on colours

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_violin()

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