componentplot {matrixcut}

Draws a Plot Showing the Number of Components as a Function of the Cutoff Value.

Description

The function takes a square sequence similarity matrix and calculates the number of independent components in which the sequence similarity between the members is greater than a specified value (between 0 and 1). It creates a plots showing the number of components corresponding to a given cutoff value. The function also depicts the inflection point with a vertical line. Upper and lower bounds can be provided between which the inflection point will be found (if it exists).

Version 0.0.1. Author: Dr. Matthew Cserhati Email: [e-mail] March 19, 2023

Arguments

mx

a square sequence similarity matrix

lower_bound

lower bounds for calculating the inflection point in, default = 0

upper_bound

upper bounds for calculating the inflection point in, default = 1

Value

A plot showing the number of components as a function of the cutoff threshold.

References

Mullner. <ArXiv:1109.2378>

Cserhati, Carter. (2020, Journal of Creation 34(3):41-50), <https://dl0.creation.com/articles/p137/c13759/j34-3_64-73.pdf>

Examples

componentplot(xenarthra,0.75,0.9)
componentplot(xenarthra)