inGraphs {InPosition}

inGraphs: InPosition plotting function

Description

InPosition plotting function which is an interface to prettyGraphs.

Usage

inGraphs(res, DESIGN = NULL, x_axis = NULL, y_axis = NULL, inference.info = NULL, 
color.by.boots = TRUE, boot.cols = c("plum4", "darkseagreen", "firebrick3"), 
fi.col = NULL, fi.pch = NULL, fj.col = NULL, fj.pch = NULL, col.offset = NULL,
constraints = NULL, xlab = NULL, ylab = NULL, main = NULL, bootstrapBars = TRUE, 
correlationPlotter = TRUE, biplots = FALSE)

Arguments

res

results from InPosition or ExPosition. If results are from ExPosition, inference.info must be included.

DESIGN

A design matrix to apply colors (by pallete selection) to row items

x_axis

which component should be on the x axis?

y_axis

which component should be on the y axis?

inference.info

Inference data as output by InPosition (of class inpoOutput).

color.by.boots

a boolean. If TRUE, items are colored by bootstrap ratio test. Items larger than critical.value are colored 'plum4' on the horizontal component, 'darkseagreen' on the vertical component, or 'firebrick3' if the item is significant on both components (to be visualized). If FALSE, the color of the items will be used.

boot.cols

vector of colors: c(horizontal component color, vertical component color, color when item is significant on both).

fi.col

A matrix of colors for the row items. If NULL, colors will be selected.

fi.pch

A matrix of pch values for the row items. 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.

xlab

x axis label

ylab

y axis label

main

main label for the graph window

bootstrapBars

a boolean. If TRUE (default), bootstrap ratio 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).

biplots

a boolean. If FALSE (default), separate plots are made for row items ($fi) and column items ($fj). If TRUE, row ($fi) and column ($fj) items will be on the same plot.

Value

Currently, nothing is returned. This function, for now, works as a visualizer for inference tests. Colors and constraints come from the descriptive (fixed effects) analysis.

Author(s)

Derek Beaton

See Also

epGraphs

Examples

	data(ep.iris)
	data<-ep.iris$data
	design<-ep.iris$design
	gpca.iris.res <- epGPCA.inference.battery(data,DESIGN=design,make_design_nominal=FALSE)
	inGraphs(gpca.iris.res,y_axis=3)