create_pca {wilson}

Method for pca creation.

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).