plot_umap: Plot results of UMAP

In jcalendo/coriell: Convenience Functions for Bioinformatics

Plot results of UMAP

Description

This function creates a simple plot of the data.frame returned by the umap() function.

Usage

plot_umap(
  df,
  x = "UMAP1",
  y = "UMAP2",
  colBy = NULL,
  shapeBy = NULL,
  pointSize = 3,
  pointAlpha = 1,
  hline = 0,
  vline = 0,
  hlineType = 2,
  vlineType = 2
)

Arguments

df	data.frame of UMAP embeddings and metadata
x	First UMAP component. Default "UMAP1"
y	Second UMAP component. Default "UMAP2"
colBy	Column name of data.frame to color points by. Default NULL
shapeBy	Column name of data.frame to shape the points by. Default NULL
pointSize	Size of the points. Default 3
pointAlpha	Alpha level of the points. Default 1
hline	y-position of horizontal line. Default 0
vline	x-position of vertical line. Default 0
hlineType	linetype of the horizontal line. Default 2
vlineType	linetype of the vertical line. Default 2

Value

ggplot object

Examples

# Create metadata for plotting
metadata <- data.frame(row.names = colnames(GSE161650_lc))
metadata$Group <- rep(c("DMSO", "THZ1"), each = 3)

# PCA with PCAtools
p <- PCAtools::pca(GSE161650_lc, metadata, center = TRUE, scale = TRUE)
udata <- coriell::UMAP(p, n_neighbors = 2)
plot_umap(udata, colBy = "Group")

jcalendo/coriell documentation built on March 5, 2025, 5:42 a.m.