tepGraphs: tepGraphs: TExPosition plotting function

Description

TExPosition plotting function which is an interface to prettyGraphs.

Usage

tepGraphs(
  res,
  x_axis = 1,
  y_axis = 2,
  tepPlotInfo = NULL,
  DESIGN = NULL,
  fi.col = NULL,
  fi.pch = NULL,
  fii.col = NULL,
  fii.pch = NULL,
  fj.col = NULL,
  fj.pch = NULL,
  col.offset = NULL,
  constraints = NULL,
  lv.constraints = NULL,
  xlab = NULL,
  ylab = NULL,
  main = NULL,
  lvPlots = TRUE,
  lvAgainst = TRUE,
  contributionPlots = TRUE,
  correlationPlotter = TRUE,
  showHulls = 1,
  graphs = TRUE
)

Value

The following items are bundled inside of $Plotting.Data:

$fii.col: the colors that are associated to the individuals (row items; $fii).
$fii.pch: the pch values associated to the individuals (row items; $fii).
$fi.col: the colors that are associated to the groups ($fi).
$fi.pch: the pch values associated to the groups ($fi).
$fj.col: the colors that are associated to the column items ($fj).
$fj.pch: the pch values associated to the column items ($fj).
$constraints: axis constraints for the plots (determines end points of the plots).

Arguments

res: results from TExPosition
x_axis: which component should be on the x axis?
y_axis: which component should be on the y axis?
tepPlotInfo: A list ($Plotting.Data) from tepGraphs or TExPosition.
DESIGN: A design matrix to apply colors (by pallete selection) to row items
fi.col: A matrix of colors for the group items. If NULL, colors will be selected.
fi.pch: A matrix of pch values for the group items. If NULL, pch values are all 21.
fii.col: A matrix of colors for the row items (observations). If NULL, colors will be selected.
fii.pch: A matrix of pch values for the row items (observations). If NULL, pch values are all 21.
fj.col: A matrix of colors for the column items. If NULL, colors will be selected.
fj.pch: A matrix of pch values for the column items. If NULL, pch values are all 21.
col.offset: A numeric offset value. Is passed to createColorVectorsByDesign.
constraints: Plot constraints as returned from prettyPlot. If NULL, constraints are selected.
lv.constraints: Plot constraints for latent variables. If NULL, constraints are selected.
xlab: x axis label
ylab: y axis label
main: main label for the graph window
lvPlots: a boolean. If TRUE, latent variables (X, Y) are plotted. If FALSE, latent variables are not plotted.
lvAgainst: a boolean. If TRUE, latent variables (X, Y) are plotted against each other. If FALSE, latent variables are plotted like factor scores.
contributionPlots: a boolean. If TRUE (default), contribution bar plots will be created.
correlationPlotter: a boolean. If TRUE (default), a correlation circle plot will be created. Applies to PCA family of methods (CA is excluded for now).
showHulls: a value between 0 and 1 to make a peeled hull at that percentage. All values outside of 0-1 will not plot any hulls.
graphs: a boolean. If TRUE, graphs are created. If FALSE, only data associated to plotting (e.g., constraints, colors) are returned.

Author

Derek Beaton

Details

tepGraphs is an interface between TExPosition and prettyGraphs.

Examples

Run this code


	#this is for TExPosition's iris data
	data(ep.iris)
	bada.iris <- tepBADA(ep.iris$data,DESIGN=ep.iris$design,
	  make_design_nominal=FALSE,graphs=FALSE)
	#there are only 2 components, not 3.		
	bada.iris.plotting.data <- tepGraphs(bada.iris,x_axis=1,y_axis=2)

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