TDApplied (version 3.0.3)

plot_diagram: Plot persistence diagrams

Description

Plots a persistence diagram outputted from either a persistent homology calculation or from diagram_to_df, with maximum homological dimension no more than 12 (otherwise the legend doesn't fit in the plot). Each homological dimension has its own color (the rcartocolor color-blind safe color palette) and point type, and the main plot title can be altered via the `title` parameter. Each feature is plotted with a black point at its center in order to distinguish between overlapping features and easily compare features to their persistence thresholds.

Usage

plot_diagram(
  D,
  title = NULL,
  max_radius = NULL,
  legend = TRUE,
  thresholds = NULL
)

Arguments

D

a persistence diagram, either outputted from either a persistent homology homology calculation like ripsDiag/calculate_homology/PyH or from diagram_to_df, with maximum dimension at most 12.

title

the character string plot title, default NULL.

max_radius

the x and y limits of the plot are defined as `c(0,max_radius)`, and the default value of `max_radius` is the maximum death value in `D`.

legend

a logical indicating whether to include a legend of feature dimensions, default TRUE.

thresholds

either a numeric vector with one persistence threshold for each dimension in `D` or the output of a bootstrap_persistence_thresholds function call, default NULL.

Author

Shael Brown -

Details

The `thresholds` parameter, if not NULL, can either be a user-defined numeric vector, with one entry (persistence threshold) for each dimension in `D`, or the output of bootstrap_persistence_thresholds. Points whose persistence are greater than or equal to their dimension's threshold will be plotted in their dimension's color, and in gray otherwise.

Examples

if(require("TDAstats"))
{
  # create a sample diagram from the unit circle
  df <- TDAstats::circle2d[sample(1:100,50),]
  diag <- TDAstats::calculate_homology(df,threshold = 2)

  # plot without title
  plot_diagram(diag)

  # plot with title
  plot_diagram(diag,title = "Example diagram")

  # determine persistence thresholds
  thresholds <- bootstrap_persistence_thresholds(X = df,maxdim = 1,
  thresh = 2,num_samples = 3,
  num_workers = 2)

  # plot with bootstrap persistence thresholds
  plot_diagram(diag,title = "Example diagram with thresholds",thresholds = thresholds)

  #' # plot with personalized persistence thresholds
  plot_diagram(diag,title = "Example diagram with personalized thresholds",thresholds = c(0.5,1))
}