plot_umap: UMAP plot

In pengminshi/cFIT: cFIT (common Factor Space Integration & Transfer)

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
alpha	numeric, transparency of the points in the plot
title	string, title of the plot
legend.name	string, legend name
cols	vector of colors, length should the same as cardinality of labels
emb	embedding of the UMAP if provided
seed	random seed

Value

A list of

p

umap plot

emb

umap embedding matrix

pengminshi/cFIT documentation built on July 11, 2021, 11:12 p.m.