create_pca: Method for pca creation.

In wilson: Web-Based Interactive Omics Visualization

Description

Method for pca creation.

Usage

create_pca(
  data,
  color.group = NULL,
  color.title = NULL,
  palette = NULL,
  shape.group = NULL,
  shape.title = NULL,
  shapes = c(15:25),
  dimension.a = 1,
  dimension.b = 2,
  dimensions = 6,
  on.columns = TRUE,
  labels = FALSE,
  custom.labels = NULL,
  pointsize = 2,
  labelsize = 3,
  width = 28,
  height = 28,
  ppi = 72,
  scale = 1
)

Arguments

data	data.table from which the plot is created (First column will be handled as rownames if not numeric).
color.group	Vector of groups according to samples (= column names).
color.title	Title of the color legend.
palette	Vector of colors used for color palette.
shape.group	Vector of groups according to samples (= column names).
shape.title	Title of the shape legend.
shapes	Vector of shapes see points. Will recycle/ cut off shapes if needed. Default = c(15:25)
dimension.a	Number of dimension displayed on X-Axis.
dimension.b	Number of dimension displayed on Y-Axis.
dimensions	Number of dimensions to create.
on.columns	Boolean perform pca on columns or rows.
labels	Boolean show labels.
custom.labels	Vector of custom labels. Will replace columnnames.
pointsize	Size of the data points.
labelsize	Size of texts inside plot (default = 3).
width	Set the width of the plot in cm (default = 28).
height	Set the height of the plot in cm (default = 28).
ppi	Pixel per inch (default = 72).
scale	Modify plot size while preserving aspect ratio (Default = 1).

Details

If width and height are the same axis ratio will be set to one (quadratic plot).

Width/ height limit = 500. If exceeded default to 500 and issue exceed_size = TRUE.

Value

A named list(plot = ggplot object, data = pca.data, width = width of plot (cm), height = height of plot (cm), ppi = pixel per inch, exceed_size = Boolean whether width/ height exceeded max).

wilson documentation built on April 19, 2021, 5:07 p.m.