plot_umap: Dimensional reduction plot with expression overlaid

In jackbibby1/scExpression: Plot single cell expression data

Description

Use this to overlay expression of RNA or proteins on a UMAP/tSNE plot

Usage

plot_umap(
  dataset,
  genes,
  rna_protein = "rna",
  reduction = "umap",
  min_cutoff = 0.5,
  max_cutoff = 3,
  split_condition = T,
  add_cell_label = T,
  avoid_overlap = T
)

Arguments

dataset	Seurat object that you want to get expression from
genes	The genes you want to plot
rna_protein	Do you want to plot the RNA or protein expression?
reduction	Do you want a UMAP or tSNE?
min_cutoff	Don't show anything below this expression level
max_cutoff	Set this as maximum on the expression level scale
split_condition	Do you want to split the plots by disease?
add_cell_label	Should cell names be added to UMAP as well as legend
avoid_overlap	Force cell names to avoid overalpping on UMAP

Examples

## Not run: 
plot_umap(dataset = seurat_object,
          genes = "IFNG",
          reduction = "tnse",
          min_cutoff = 1)

## End(Not run)

jackbibby1/scExpression documentation built on Dec. 20, 2021, 8:05 p.m.