Feature-class {RPointCloud}

Feature Objects For Visualizing Topological Data Anal;ysis Results

Description

The Feature object represents a feature from a data matrix used when performing topological data analysis with the TDA package. Features might be genes, proteins, clinical or demographic covariates, or any other item measured on a set of patient samples or cells.

Usage

Feature(values, name, colors, meaning, ...)
## S4 method for signature 'Feature,matrix'
plot(x, y, pch = 16, ...)
## S4 method for signature 'Feature'
points(x, view, ...)

Arguments

values

A numeric vector.

name

A character vector of length one.

colors

A character vector of length at least two, containing the names or hexadecimal representations of colors used to create a color ramp to display the feature.

meaning

A character vector of length two containing the interpretations of the low and high extreme values of the feature. Note that this works perfectly well for binary factors represented as numeric 0-1 vectors.

x

A Feature object.

y

A (layout) matrix with coordinates showing where to plot each point in the feature.

view

A (layout) matrix with coordinates showing where to plot each point in the feature.

pch

A number; the graphical plotting character parameter pch.

...

The usual set of additional graphical parameters.

Value

The Feature function constructs and returns an object of the Feature class

The plot and points methods return (invisibly) the Feature object that was their first argument.

Slots

name:

A character vector of length one; the name of the feature..

values:

A numeric vector of the values of this feature.

meaning:

A character vector of length two containing the interpretations of the low and high extreme values of the feature. Note that this works perfectly well for binary factors represented as numeric 0-1 vectors.

colRamp:

A function created using the colorRamp2 function from the circlize package.

Methods

plot(x, y, lwd = 2, ...):

Produce a plot of a Feature object.

points(x, view, ...)

Add a depiction of a feature to an existing plot.

Author(s)

Kevin R. Coombes <[e-mail]>

Examples

data(CLL)
featSex <- Feature(clinical[,"Sex"], "Sex",
            c("pink", "skyblue"), c("Female", "Male"))
V <- cmdscale(daisydist)
plot(featSex, V)
plot(V)
points(featSex, V)