TDAstats (version 0.4.1)

plot_persist: Plot Persistent Homology as Persistence Diagram

Description

Plots a feature matrix as a persistence diagram. See `plot_barcode` for an alternate visualization method of persistent homology.

Usage

plot_persist(feature.matrix, flat = FALSE, cutoff = 0)

Arguments

feature.matrix

nx3 matrix representing persistent homology features

flat

default FALSE; if TRUE, plots flat persistent homology instead

cutoff

threshold for significant features; line added as marker on plot

Value

ggplot instance representing persistence diagram

Details

The `feature.matrix` parameter should be a numeric matrix with each row corresponding to a single feature. It should have 3 columns corresponding to feature dimension (col 1), feature birth (col 2), and feature death (col 3). The first column should be filled with integers, and the next two columns should be filled with numeric values. The output from the `calculate_homology` function in this package will be a valid value for the `feature.matrix` parameter.

This function uses the ggplot2 framework to generate persistence diagrams. For details, see: Wickham H (2009, ISBN:9780387981413). ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag: New York, NY.

Examples

# NOT RUN {
# create a 2-d point cloud of a circle (100 points)
num.pts <- 100
rand.angle <- runif(num.pts, 0, 2*pi)
pt.cloud <- cbind(cos(rand.angle), sin(rand.angle))

# calculate persistent homology (num.pts by 3 numeric matrix)
pers.hom <- calculate_homology(pt.cloud)

# plot calculated homology features as persistence diagram
plot_persist(pers.hom)
# }