plot_UMAP_marker: Colouring UMAP results with marker expressions

In desmchoy/BinaryClust: CyTOF Analysis Pipeline Using Binary Classification Followed by Clustering

Colouring UMAP results with marker expressions

Description

This function colours UMAP results by marker expressions. Returns a graph.

Usage

plot_UMAP_marker(
  umap.results = NULL,
  data = NULL,
  marker = NULL,
  lower = NULL,
  upper = NULL,
  palette = "Purples",
  title = ""
)

Arguments

umap.results	(Required) UMAP object. Expects results from run_UMAP
data	(Required) Data in data frame format. Expects results from load_data
marker	(Required) Marker to be coloured
lower	Lower bound of colour spectrum (Default: Lowest value of marker expression)
upper	Upper bound of colour spectrum (Default: Highest value of marker expression)
palette	ggplot2 colour spectrum (Default: 'Purples')
title	Title of plot (Default: NULL)

Examples

plot_UMAP_marker(umap.results, data, marker = 'CD45')

desmchoy/BinaryClust documentation built on Sept. 14, 2024, 12:03 a.m.