cms_biplot: cms_biplot
In schyen/OCMSExplorer: OCMSlooksy

cms_biplot

R Documentation

cms_biplot

Description

Modification of ggfortify::ggbiplot to allow for variables in aes_string (not just colour specification)

Usage

cms_biplot(
  plot.data,
  loadings.data = NULL,
  colour = NULL,
  size = NULL,
  linetype = NULL,
  alpha = NULL,
  fill = NULL,
  shape = NULL,
  label = FALSE,
  label.label = "rownames",
  label.colour = colour,
  label.alpha = NULL,
  label.size = NULL,
  label.angle = NULL,
  label.family = NULL,
  label.fontface = NULL,
  label.lineheight = NULL,
  label.hjust = NULL,
  label.vjust = NULL,
  label.repel = FALSE,
  loadings = FALSE,
  loadings.colour = "#FF0000",
  loadings.shape = NULL,
  loadings.size = NULL,
  loadings.alpha = NULL,
  loadings.arrow = FALSE,
  loadings.label = FALSE,
  loadings.label.label = "rownames",
  loadings.label.colour = "#FF0000",
  loadings.label.alpha = NULL,
  loadings.label.size = NULL,
  loadings.label.angle = NULL,
  loadings.label.family = NULL,
  loadings.label.fontface = NULL,
  loadings.label.lineheight = NULL,
  loadings.label.hjust = NULL,
  loadings.label.vjust = NULL,
  loadings.label.repel = FALSE,
  label.show.legend = NA,
  frame = FALSE,
  frame.type = NULL,
  frame.colour = colour,
  frame.line = "solid",
  frame.level = 0.95,
  frame.alpha = 0.2,
  xlim = c(NA, NA),
  ylim = c(NA, NA),
  log = "",
  main = NULL,
  xlab = NULL,
  ylab = NULL,
  asp = NULL,
  ...
)

Arguments

`plot.data`	score data, samples in rows
`colour`	colour of score points. default NULL
`size`	size of score points. default NULL
`linetype`	line type of arrows to points. default NULL
`alpha`	alpha of score points. default NULL
`fill`	fill of score points. default NULL
`shape`	shape of score points.default NULL
`label`	show score labels. default FALSE
`label.label`	name of column to be used to label scores. default 'rownames'
`label.colour`	colour of score labels
`label.alpha`	alpha of score labels default NULL
`label.size`	size of score labels. default NULL
`label.angle`	angle fo score labels. default NULL
`label.family`	font of score labels. default NULL
`label.fontface`	fontface of score labels. default NULL
`label.lineheight`	lineheight of score labels. default FALSE
`label.hjust`	hjust of score labels. default NULL
`label.vjust`	vjsut of score labels, default NULL
`label.repel`	use ggrepel for score labels. default FALSE
`loadings`	show loadings. default FALSE
`loadings.colour`	colour of loadings. default red (#FF0000)
`loadings.shape`	shape of loadings. default NULL
`loadings.size`	size of loadings. default NULL
`loadings.alpha`	alpha of loadings. default NULL
`loadings.arrow`	show line to loadings. default FALSE
`loadings.label`	show labels for loadings. default FALSE
`loadings.label.label`	column used to label loadings. default 'rownames'
`loadings.label.colour`	colour of loading label. default red (#FF0000)
`loadings.label.alpha`	alpha of loading label default NULL
`loadings.label.size`	size of loading label. default NULL
`loadings.label.angle`	angle of loadings label. default NULL
`loadings.label.family`	font of loading labels. default NULL
`loadings.label.fontface`	fontface of loading labels. default NULL
`loadings.label.hjust`	hjust of loading labels. default NULL
`loadings.label.vjust`	vjust of loading labels. defualt NULL
`loadings.label.repel`	use ggrepel on loading labels. default FALSE
`label.show.legend`	show legend labels. default NA
`frame`	frame clusters based on confidence interval estimation default FALSE
`frame.type`	type of CI estimation. must one of: `convex, t, norm or euclid` default NULL
`frame.colour`	frame colour. default `colour`
`frame.line`	frame linetype. default `'solid'`
`frame.level`	frame lineweight. default `0.95`
`frame.alpha`	frame alpha. default `0.2`
`xlim`	x-axis limits default `c(NA, NA)`
`ylim`	y-axis limits default `c(NA, NA)`
`log`	default ”
`main`	plot title. default NULL
`xlab`	x-axis title. default NULL
`ylab`	y-axis title. default NULL
`asp`	default NULL
`loadings_data`	loading data, features in rows