tepGraphs {TExPosition}

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, biplots = FALSE, graphs = TRUE)

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.

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.

Details

tepGraphs is an interface between TExPosition and prettyGraphs.

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).

Author(s)

Derek Beaton

See Also

prettyGraphs

Examples

	#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)