prettyPlot: prettyPlot
In prettyGraphs: Publication-Quality Graphics

Description Usage Arguments Details Value Author(s)

View source: R/prettyPlot.R

prettyPlot creates simple, crisp, publication-style quality graphics for multivariate analyses.

prettyPlot(data_matrix,x_axis=1,y_axis=2,col=NULL,pch=NULL,cex=NULL,text.cex=NULL,
	pos=3,xlab="",ylab="",main="",display_names=TRUE,display_points=TRUE,
	constraints=NULL,contributionCircles=FALSE,contributions=NULL,axes=TRUE,
	fg.line.width=3,fg.type="l",fg.col="black",
	bg.line.width=1.5,bg.lty=3,bg.col="black",
	flip=FALSE,asp=1,findBounds=TRUE,dev.new=TRUE,new.plot=TRUE)

`data_matrix`	A set of data you would like to plot on 2 dimensions (e.g., a scatter plot). Can be original data or factor scores or anything with at least 2 columns.
`x_axis`	Which axis is the x-axis? Default is 1.
`y_axis`	Which axis is the y-axis? Default is 2.
`col`	any acceptable color format. A single-column matrix of colors for each data point. A single value can be used.
`pch`	A single-column matrix of pch for each data point. A single value can be used. Indicates which point style to use for each item. See `par`.
`cex`	a single column of continuous values. A single value can be used. Indicates the size of the points. See `par`. Used multiplicatively for points with `contributions`.
`text.cex`	A replacement for the cex parameter in text() (to avoid collisions with cex). Used additively for points with `contributions`. See `par` and `text`.
`pos`	integer between 1-4. Determines position of text for points. See `par`.
`xlab`	A label to be placed along the x-axis.
`ylab`	A label to be placed along the y-axis.
`main`	A title to be placed at the top of the graph.
`display_names`	boolean. If TRUE, the names of the points will be displayed on the plot.
`display_points`	boolean. If TRUE, the points will be displayed on the plot.
`constraints`	A list that contains the plot constraints. Default is NULL (constraints are computed each time).
`contributionCircles`	boolean. If TRUE, items plotted will vary in size, dependent on amount of contribution to the variance.
`contributions`	A matrix of contribution values for data_matrix (should also be the same size & dimensionality as data_matrix)
`axes`	boolean. If TRUE, a new set of axes are plotted.
`fg.line.width`	integer. Determines thickness of foreground (default: solid) axis lines, see `points` and `lwd` under `par`.
`fg.type`	character or string Determines type of points for foreground (default: solid) axis lines, see `points` and `type` under `par`.
`fg.col`	any acceptable color format. Determines color for foreground (default: solid) axis lines, see `points` and `col` under `par`.
`bg.line.width`	integer. Determines thickness of background (default: dashed) axis lines, see `abline` and `lwd` under `par`.
`bg.lty`	integer. Determines type of background (default: dashed) axis lines, see `abline` and `lty` under `par`.
`bg.col`	any acceptable color format. Determines color of background (default: dashed) axis lines, see `abline` and `col` under `par`.
`flip`	boolean. If TRUE, exchanges bg and col for all applicable pch values.
`asp`	numeric. Aspect ratio, see `par`.
`findBounds`	boolean. If TRUE, finds the min and max of each plotted axes. If FALSE, the largest value is used for all constraints.
`dev.new`	boolean. If TRUE, `dev.new` is called internally to create new device. If FALSE, a device must already be open.
`new.plot`	boolean. If TRUE, `plot` is called for a new plot on the current device. If FALSE, items will be overlayed much like `points`.

All items after contributions (i.e., axes onward) are parameters for very fine-grained detail. They are quite powerful but in most cases not required.

Returns a three item list:

`col`	A matrix of colors where each element is the color for each item plotted.
`pch`	A matrix of pch values where each element is the pch number for each item plotted.
`constraints`	A list (from `minmaxHelper`) of the plot constraints (i.e., min and max for axes)