m09-voids.R: 3D Scatter Plots of Cycles and Features

In Mender: Visualizing Topological Loops and Voids

3D Scatter Plots of Cycles and Features

Description

Voids are two-dimensional cycles and should be thought of as the topological equivalents of (the surface) of a sphere. These are typically displayed as a point cloud in space, with wire-frame edges outlining the component (triangular) simplices.

Usage

voidPlot(cycle, view, feature = NULL, radius = 0.01, ...)
voidFeature(feature, view, radius = 0.01, ...)

Arguments

cycle	An object of the Cycle class.
view	A matrix (with three columns, x, y, and, z) specifying the coordinates to be used to display the data.
feature	An object of the Feature class.
radius	The radius of spheres used to display the points in three dimensions.
...	Additional graphical parameters.

Details

The 3D displays are implemented using the rgl package. The voidPlot function adds a wire-frame two-cycle to the 3d scatter plot of the underlying data. If a feature is present, then the point are colored by the expression lecvel of that feature. If not present, they are simply colored gray. However, you can always add the expression levels of a feature to an existing plot using the voidFeature function.

In an interactive session, everything is displayed in an OpenGL window, where the graph can be manipulated with a mouse. Programmatically, you can use the rgl::rglwidget function to write out the code for an interactive HTML display, and you can save the widget to a file using the htmlwidgets::saveWidget function.

Value

Both voidPlot and voidFeature invisibly return their first argument.

Author(s)

Kevin R. Coombes <[e-mail]>

Examples

data(CLL)
featRai <- Feature(clinical[,"CatRAI"], "Rai Stage", c("green", "magenta"), c("High", "Low"))
vd <- Cycle(ripdiag, 2, 95, "blue")
mds <- cmdscale(daisydist, k = 3)
voidPlot(vd, mds)
voidFeature(featRai, mds, radius = 0.011)

Mender documentation built on Oct. 25, 2023, 3 a.m.