plot_pcs: Plot principle components and make them pretty.

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

Plot principle components and make them pretty.

Description

All the various dimension reduction methods share some of their end-results in common. Most notably a table of putative components which may be plotted against one another so that one may stare at the screen and look for clustering among the samples/genes/whatever. This function attempts to make that process as simple and pretty as possible.

Usage

plot_pcs(
  pca_data,
  first = "PC1",
  second = "PC2",
  variances = NULL,
  design = NULL,
  plot_title = TRUE,
  plot_labels = NULL,
  x_label = NULL,
  y_label = NULL,
  plot_size = 5,
  outlines = TRUE,
  plot_alpha = NULL,
  size_column = NULL,
  rug = TRUE,
  max_overlaps = 20,
  cis = c(0.95, 0.9),
  ellipse_type = "t",
  ellipse_geom = "polygon",
  label_size = 4,
  ...
)

Arguments

pca_data	Dataframe of principle components PC1 .. PCN with any other arbitrary information.
first	Principle component PCx to put on the x axis.
second	Principle component PCy to put on the y axis.
variances	List of the percent variance explained by each component.
design	Experimental design with condition batch factors.
plot_title	Title for the plot.
plot_labels	Parameter for the labels on the plot.
x_label	Label for the x-axis.
y_label	Label for the y-axis.
plot_size	Size of the dots on the plot
outlines	Add a black outline to the plotted shapes?
plot_alpha	Add an alpha channel to the dots?
size_column	Experimental factor to use for sizing the glyphs
rug	Include the rugs on the sides of the plot?
max_overlaps	Increase overlapping label tolerance.
cis	What (if any) confidence intervals to include.
ellipse_type	Choose the kernel for the ellipse.
ellipse_geom	Use this ggplot geometry.
label_size	The text size of the labels.
...	Extra arguments dropped into arglist

Value

gplot2 PCA plot

See Also

[directlabels] [ggplot2] [plot_pca] [pca_information]

Examples

## Not run: 
 pca_plot = plot_pcs(pca_data, first = "PC2", second = "PC4", design = expt$design)

## End(Not run)

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