plotUMAP: Plot UMAP embeddings

In plantformatics/Socrates: Analysis of scATAC-seq data

Plot UMAP embeddings

Description

Function to plot UMAP embeddings using meta data to establish cell colors.

Usage

plotUMAP(
  obj,
  column = "LouvainClusters",
  cex = 0.3,
  opaque = 1,
  cluster_slotName = "Clusters",
  xlab = "umap1",
  ylab = "umap2",
  main = "",
  ...
)

Arguments

obj	list, object containing meta data.
column	character, column header specifying how to color cells. Factors are plotted catagorically, while continuous numeric values are plotted along a spectrum.
cex	float, set the point size. Defaults to 0.3.
opaque	float, set the transparency of point colors. Defaults to 1.
cluster_slotName	character, string specifying the desired meta slot to use for plotting. Defaults to "Clusters". If callClusters hasnt been run (or is missing from the object), slot meta is used instead.
xlab	character string for x-axis name.
ylab	character string for y-axis name.
main	character string for graph title.
...	other arguments accepted by 'plot'.

plantformatics/Socrates documentation built on April 3, 2025, 1:02 p.m.