Plot Cells Reduced Dimensions With Gene Expression — plot_reduced_dim_gene • scFlow

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

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

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_violin()