embed: Embed Manifold

In dswatson/bioplotr: Pretty, simple, optionally interactive plots for bioinformatics analysis pipelines

Embed Manifold

Description

This utility function formats the output for bioplotr's projection functions (plot_pca, plot_mds, and plot_tsne).

Usage

embed(
  df,
  group,
  covar,
  group_cols,
  covar_cols,
  feature_names,
  label,
  size,
  alpha,
  title,
  xlab,
  ylab,
  legend,
  hover,
  D3
)

Arguments

df	Data frame formatted for ggploting.
group	Optional factor variable formatted by format_features.
covar	Optional continuous variable formatted by format_features.
group_cols	Palette for group formatted by colorize.
covar_cols	Palette for covar formatted by colorize.
feature_names	Feature names.
label	Label data points by sample name?
title	Plot title.
xlab	X-axis label.
ylab	Y-axis label.
legend	Legend location.
hover	Show sample name by hovering mouse over data point?
D3	Render plot in three dimensions?

dswatson/bioplotr documentation built on March 3, 2023, 9:43 p.m.