picketPlotControl: Default parameter settings for picketPlot

In alexploner/Heatplus: Heatmaps with row and/or column covariates and colored clusters

Description

This function returns a named list of parameters that affect how a picketPlot is generated. This list can be used as a template for overriding the defaults partially or completely.

Usage

picketPlotControl()

Details

The following parameter affects the overall appearance of the plot:

• cex.label is the expansion factor for the size of the cluster labels at the bottom of the plot; default is 1.5.

The following parameters directly affect how binary indicator variables are displayed:

• boxw is the relative length of the short side of a box marking (width for a horizontal plot); default is 1.

• boxh is the relative length of the long side of a box marking (default: 4)

• hbuff is the relative distance between two box markings for the same variable (horizontal buffer for a horizontal plot); default is 0.1

• vbuff is the relative distance between two box markings for the same subject, but different variables (default: 0.1)

• nacol is the color for box markings indicating missing values (default: gray(0.85))

Note that boxh and vbuff also affect the display of numerical variables as a scatter plot: as the amount of vertical space allowed for a single numerical variable (see also numfac below) and the vertical space between two neighboring variable panels (binary or ornumerical), respectively.

The following parameters only affect the display of a numerical variable:

• numfac is the expansion factor indicating how much higher (for a horizontal plot) or wider (for a vertical plot) panels with numerical variables are than a panels for a single binary indicator

• span is the span argument for the loess smoother. Default is 1/3; setting this to zero switches off smoothing.

• degree is the degree of loess smoothing. Default is 1; setting this to zero switches off smoothing

• pch is the plotting character for numerical variables; uses the device default.

• cex.pch is the size of the plotting character for numerical variables; uses the device default.

• col.pch is the color of the plotting character for numerical variables; uses the device default.

• label_axis_shrink controls the range of the axis for which axis ticks are labeled: by default, labels covering the whole observed range are defined (via a call to pretty); if set to a number between zero and one, the range covered by labels is shortened by that fraction and centered within the observed range (and the fed to pretty); this can be used to avoid overlapping labels for multiple adjacent panes with numerical variables.

• plot_baseline is a logical value indicating whether to draw a baseline for panes showing numerical variables: FALSE by default, this can be useful to visually separate multiple adjacent panes with numerical variables.

Value

A named list

See Also

picketPlot, par, pretty

alexploner/Heatplus documentation built on May 23, 2021, 2:01 p.m.