plot_pca: Make a PCA plot describing the samples' clustering.

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

Make a PCA plot describing the samples' clustering.

Description

Make a PCA plot describing the samples' clustering.

Usage

plot_pca(
  data,
  design = NULL,
  plot_colors = NULL,
  plot_title = TRUE,
  plot_size = 5,
  plot_alpha = NULL,
  plot_labels = FALSE,
  size_column = NULL,
  pc_method = "fast_svd",
  x_pc = 1,
  y_pc = 2,
  max_overlaps = 20,
  num_pc = NULL,
  expt_names = NULL,
  label_chars = 10,
  cond_column = "condition",
  batch_column = "batch",
  ...
)

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.
max_overlaps	Passed to ggrepel.
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.
cond_column	Column containing the color information.
batch_column	Column containing the shape information.
...	Arguments passed through to the pca implementations and plotter.

Value

a list containing the following (this is currently wrong)

1. pca = the result of fast.svd()

2. plot = ggplot2 pca_plot describing the principle component analysis of the samples.

3. table = a table of the PCA plot data

4. res = a table of the PCA res data

5. variance = a table of the PCA plot variance

See Also

[corpcor] [Rtsne] [uwot] [fastICA] [pcaMethods] [plot_pcs()]

Examples

## Not run: 
 pca_plot <- plot_pca(expt = expt)
 pca_plot

## End(Not run)

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