plotly_pca: Plot a PC plot with options suitable for ggplotly.

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Plot a PC plot with options suitable for ggplotly.

Description

Plot a PC plot with options suitable for ggplotly.

Usage

plotly_pca(
  data,
  design = NULL,
  plot_colors = NULL,
  plot_title = NULL,
  plot_size = 5,
  plot_alpha = NULL,
  plot_labels = NULL,
  size_column = NULL,
  pc_method = "fast_svd",
  x_pc = 1,
  y_pc = 2,
  outlines = FALSE,
  num_pc = NULL,
  expt_names = NULL,
  label_chars = 10,
  tooltip = c("shape", "fill", "sampleid"),
  ...
)

Arguments

data	an expt set of samples.
design	a design matrix and.
plot_colors	a color scheme.
plot_title	a title for the plot.
plot_size	size for the glyphs on the plot.
plot_alpha	Add an alpha channel to the dots?
plot_labels	add labels? Also, what type? FALSE, "default", or "fancy".
size_column	use an experimental factor to size the glyphs of the plot
pc_method	how to extract the components? (svd
x_pc	Component to put on the x axis.
y_pc	Component to put on the y axis.
outlines	Include black outlines around glyphs?
num_pc	How many components to calculate, default to the number of rows in the metadata.
expt_names	Column or character list of preferred sample names.
label_chars	Maximum number of characters before abbreviating sample names.
tooltip	Which columns to include in the tooltip.
...	Arguments passed through to the pca implementations and plotter.

Value

This passes directly to plot_pca(), so its returns should be applicable along with the result from ggplotly.

See Also

[plotly]

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.