inGraphs: inGraphs: InPosition plotting function
In InPosition: Inference Tests for ExPosition

Description Usage Arguments Value Author(s) See Also Examples

InPosition plotting function which is an interface to prettyGraphs.

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)

`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.

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.

Derek Beaton

epGraphs

	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)

Loading required package: prettyGraphs
Loading required package: ExPosition
[1] "It is estimated that your iterations will take 0.53 minutes."
[1] "R is not in interactive() mode. Resample-based tests will be conducted. Please take note of the progress bar."
================================================================================dev.new(): using pdf(file="Rplots1.pdf")
dev.new(): using pdf(file="Rplots2.pdf")
dev.new(): using pdf(file="Rplots3.pdf")
dev.new(): using pdf(file="Rplots4.pdf")
dev.new(): using pdf(file="Rplots5.pdf")
dev.new(): using pdf(file="Rplots6.pdf")
dev.new(): using pdf(file="Rplots7.pdf")
dev.new(): using pdf(file="Rplots8.pdf")
dev.new(): using pdf(file="Rplots9.pdf")
$col
     [,1]        
[1,] "firebrick3"
[2,] "plum4"     
[3,] "plum4"     
[4,] "firebrick3"

$pch
     [,1]
[1,]   21
[2,]   21
[3,]   21
[4,]   21

$constraints
$constraints$minx
[1] -0.5167099

$constraints$miny
[1] -0.2797892

$constraints$maxx
[1] 1.140437

$constraints$maxy
[1] 0.3182901