umapCellAnno: Produces a UMAP plot from a Seurat object that can put...

In basilkhuder/extendSC: Extends functionalities of scRNA-Seq workflows

Description

Produces a UMAP plot from a Seurat object that can put cluster cell amounts in the legend, title, or on the plot.

Usage

umapCellAnno(
  seurat.obj,
  annotation.name = NULL,
  point.size = 1,
  label.size = 10,
  title = "",
  legend.title.size = 0,
  legend.text.size = 15,
  axis.title.x.size = 15,
  axis.title.y.size = 15,
  axis.text.y.left.size = 15,
  axis.text.x.bottom.size = 15,
  counts.as.title = FALSE,
  legend = TRUE,
  cell.legend.size = 10,
  counts.in.legend = TRUE,
  use.cols = NULL
)

Arguments

annotation.name	The name of the slot that contains the Seurat clusters. Defaults to "Seurat_Assignment" first, then "seurat_clusters"
point.size	Size of the UMAP plot points
title	Title of the plot
legend.title.size	Size of the legend title
legend.text.size	Size of the legend text
axis.title.x.size	X-axis title text size
axis.title.y.size	Y-axis title text size
axis.text.x.bottom.size	Y-axis sub-text size
counts.as.title	Put the total amount of cells as the title
legend	Show the legend
cell.legend.size	Show the legend
counts.in.legend	Put the amount of cells alongside cluster name in the legend
use.cols	Use custom colors for the cell clusters
axis.text.x.left.size	X-axis sub-text size

Value

A UMAP plot

Examples

umapCellAnno(seurat.obj, annotation.name = "Seurat_Clusters")

basilkhuder/extendSC documentation built on July 23, 2021, 1:17 p.m.