ezumap: UMAP plot of first two dimensions

In jdreyf/jdcbioinfo: Joslin Diabetes Center bioinformatics utilities

UMAP plot of first two dimensions

Description

UMAP plot of first two dimensions using ggplot2.

Usage

ezumap(
  object,
  pheno.df,
  name = "umap",
  pca = TRUE,
  initial_dims = nrow(pheno.df),
  config = umap::umap.defaults,
  method = c("naive", "umap-learn"),
  preserve.seed = TRUE,
  alpha = 1,
  all.size = NULL,
  facet = NULL,
  title = NULL,
  subtitle = NULL,
  rm.leg.title = FALSE,
  labels = FALSE,
  manual.color = NULL,
  manual.shape = NULL,
  plot = TRUE,
  ...
)

Arguments

object	Matrix-like object with features (e.g. genes) as rows and samples as columns.
pheno.df	Data frame with rows as samples and columns as phenotypes.
name	Name of file to create. Set to NA to plot to screen instead of to file.
pca	logical; Whether an initial PCA step should be performed (default: TRUE)
initial_dims	integer; the number of dimensions that should be retained in the initial PCA step (default: 50)
config	object of class umap.config
method	character, implementation. Available methods are 'naive' (an implementation written in pure R) and 'umap-learn' (requires python package 'umap-learn')
preserve.seed	logical, leave TRUE to insulate external code from randomness within the umap algorithms; set FALSE to allow randomness used in umap algorithms to alter the external random-number generator
alpha	Transparency, passed to geom_point.
all.size	Passed to geom_point size parameter to give size for all points without appearing in legend. ggplot2 default is size=2.
facet	A formula with columns in pheno.df to facet by.
title	Title text; suppressed if it is NULL.
subtitle	Subtitle text; suppressed if it is NULL or title is NULL. If you'd like a subtitle but no title, set title = "".
rm.leg.title	Logical indicating if legend title should be removed.
labels	Logical, should sample labels be added next to points?
manual.color	Vector passed to scale_colour_manual for creating a discrete color scale. Vector length should be equal to number of levels in mapped variable.
manual.shape	Vector passed to scale_shape_manual for creating a discrete color scale. Vector length should be equal to number of levels in mapped variable.
plot	Logical; should plot be generated?
...	list of settings with values overwrite defaults from UMAP config or passed to aes_string.

Details

object must have colnames, and if pheno.df is given, it is checked that colnames(object)==rownames(pheno.df).

Value

Invisibly, a ggplot object. Its data element contains the first two principal components appended to pheno.df.

jdreyf/jdcbioinfo documentation built on April 15, 2024, 6:37 p.m.