tepGraphs: tepGraphs: TExPosition plotting function
In TExPosition: Two-Table ExPosition

Description Usage Arguments Details Value Author(s) See Also Examples

TExPosition plotting function which is an interface to prettyGraphs.

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, biplots = FALSE, graphs = TRUE)

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

tepGraphs is an interface between TExPosition and prettyGraphs.

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).

Derek Beaton

prettyGraphs

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