eztsne: tSNE plot of first two dimensions

In jdreyf/ezlimmaplot: Bioinformatics plots using limma and ggplot2, some from output of ezlimma

tSNE plot of first two dimensions

Description

tSNE plot of first two dimensions using ggplot2.

Usage

eztsne(
  object,
  pheno.df,
  name = "tsne",
  check_duplicates = FALSE,
  pca = TRUE,
  perplexity = min(30, round(ncol(object)/5)),
  theta = 0.5,
  seed = 123,
  initial_dims = 50,
  max_iter = 1000,
  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.
check_duplicates	logical; Checks whether duplicates are present. It is best to make sure there are no duplicates present and set this option to FALSE, especially for large datasets (default: TRUE)
pca	logical; Whether an initial PCA step should be performed (default: TRUE)
perplexity	numeric; Perplexity parameter (should not be bigger than 3 * perplexity < nrow(X) - 1, see details for interpretation)
theta	numeric; Speed/accuracy trade-off (increase for less accuracy), set to 0.0 for exact TSNE (default: 0.5)
seed	Integer seed to set for reproducility if fun="mroast", since mroast uses random simulations. Ignored if fun="fry".
initial_dims	integer; the number of dimensions that should be retained in the initial PCA step (default: 50)
max_iter	integer; Number of iterations (default: 1000)
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?
...	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/ezlimmaplot documentation built on Feb. 8, 2025, 2:25 a.m.