cluster.UMAP: UMAP stratified by cluster ID

In NMikolajewicz/scMiko: scRNAseq analysis functions. Developed using Seurat framework.

UMAP stratified by cluster ID

Description

UMAP plot with colors indicating cluster membership

Usage

cluster.UMAP(
  so,
  group.by = "seurat_clusters",
  x.label = "UMAP 1",
  y.label = "UMAP 2",
  plot.name = "UMAP",
  include.labels = T,
  reduction = "umap",
  pt.size = autoPointSize(ncol(so)),
  show.axis = T,
  ...
)

Arguments

so	Seurat Object
group.by	Character. Metadata feature to group data by. Default is 'seurat_clusters'.
x.label	Character. X axis label.
y.label	Character. Y axis label.
plot.name	Character. Plot title.
include.labels	Logical specifying wheter to plot group IDs on UMAP.
reduction	Character specifying which dimensional reduction to use (e.g., umap, pca). Default is 'umap'.
show.axis	show graph axis (omit theme_void from existing ggplot). Default is T.
...	additional arguments passed to Seurat::DimPlot().

Value

ggplot handle

NMikolajewicz/scMiko documentation built on June 28, 2023, 1:41 p.m.