plot_umap: UMAP plot

In pengminshi/MRtree: Multi-resolution Reconciled Tree

UMAP plot

Description

UMAP plot

Usage

plot_umap(
  X = NULL,
  labels = NULL,
  pca = 50,
  n_components = 2,
  n_neighbors = 30,
  min_dist = 0.1,
  point.size = 0.3,
  alpha = 1,
  title = NULL,
  legend.name = "labels",
  cols = NULL,
  emb = NULL,
  seed = 0
)

Arguments

X	n-by-p expression matrix
labels	vector of sample labels
pca	umap parameter, dimension of pca
n_components	umap parameter, dimension of low dimensional embedding space (default 2)
n_neighbors	umap parameter, number of neighbors for nearest neighbor graph
min_dist	umap parameter, minimum distance of point to its nearest neighbor in the embedding space.
point.size	numeric scalar, point size in the plot, 0.3 by default.
alpha	numeric, transparency of the points in the plot, by default alpha=1 with no transparency
title	string, title of the plot, NULL by default
legend.name	string, legend name, by default is 'labels'
cols	vector of colors, length should the same as cardinality of labels, by default NULL
emb	embedding of the UMAP if provided, by default NULL
seed	random seed, by default 0

Value

A list of

p

umap plot

emb

umap embedding matrix

pengminshi/MRtree documentation built on March 6, 2023, 4:20 p.m.