plot_tsne: plot_tsne

In gtonkinhill/panstripe: Pangenome Plots

plot_tsne

Description

Generates a tSNE plot from a gene presence/absence matrix

Usage

plot_tsne(pa, category = NULL, plot = TRUE, perplexity = 20, pcadims = 50)

Arguments

pa	binary presence/absence matrix
category	a factor vector which can be used to colour the points
plot	whether to return the plot or just the data.frame used for plotting (default=TRUE)
perplexity	the 'perplexity' argument passed to tSNE
pcadims	the number of principle components passed from the inital stage used in the main tSNE algorithm

Value

either a ggplot2 object or a 'data.frame' with the data needed to recreate the plot

Examples

sim <- simulate_pan(rate=1e-3)
plot_tsne(sim$pa)

gtonkinhill/panstripe documentation built on Feb. 27, 2025, 9:01 p.m.