plot_pca: Plots PCA with ggplot2
In nicohuttmann/pOmics: Framework for proteomics data analysis

plot_pca

R Documentation

Plots PCA with ggplot2

Description

Plots PCA with ggplot2

Usage

plot_pca(
  data_,
  x = "PC1",
  y = "PC2",
  include.variance = T,
  include.ellipses = F,
  color.by,
  color,
  fill.by,
  fill,
  shape.by,
  shape,
  size.by,
  size,
  point.transparency = 1,
  ellipse.size = 1,
  ellipse.transparency = 1,
  ellipse.linetype = 1,
  custom.theme = theme_thesis_framed_no_axis,
  aspect.ratio = 1,
  plot.center,
  axis.unit.ratio,
  expand.x.axis = c(0, 0),
  expand.y.axis = c(0, 0),
  x.axis.breaks = 1,
  y.axis.breaks = 1,
  legend.title.color,
  legend.title.shape,
  legend.title.fill,
  legend.title.size,
  legend.position = "right",
  legend.rows,
  view = T,
  input = "data_pca",
  output = "plot_pca"
)

Arguments

`data_`	data_
`x`	Principal component to plot on x-axis
`y`	Principal component to plot on y-axis
`include.variance`	add variance to axis titles
`include.ellipses`	add ellipses around data points
`color.by`	column to use for coloring data points
`color`	color
`fill.by`	column to use for filling data points
`fill`	fill (same as color if not defined)
`shape.by`	column to use for shape of data points
`shape`	shape
`size.by`	column to use for size of data points
`size`	point size (default = 1)
`point.transparency`	transparency (0-1)
`ellipse.size`	thiccness of ellipse lines (default = 1)
`ellipse.transparency`	transparency of ellipse lines (default = 1)
`ellipse.linetype`	linetype of ellipses (default = 1)
`custom.theme`	theme to use for plot
`aspect.ratio`	absolute length of x-axis/y-axis
`plot.center`	vector for center of plot
`axis.unit.ratio`	ratio between x- and y-axis units
`expand.x.axis`	expand x.axis (see scale_x_continuous)
`expand.y.axis`	expand x.axis (see scale_y_continuous)
`x.axis.breaks`	space between x-axis breaks
`y.axis.breaks`	space between y-axis breaks
`legend.title.color`	title of color legend
`legend.title.shape`	title of shape legend
`legend.title.fill`	title of fill legend
`legend.title.size`	title of size legend
`legend.position`	position of legend
`legend.rows`	(optional) number of rows legend content should be presented in
`view`	view plot
`input`	name of input data
`output`	name of output data