cutoffplot

The function takes a square sequence similarity matrix and creates a plot
showing the number of similarity values above a given cutoff value, drawn on the x-axis,
ranging from 0 to 1. 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: csmatyi@protonmail.com
March 19, 2023

The user must supply a matrix filled with similarity values. The software will search for significant differences between similarity values at different hierarchical levels. The algorithm will return a Loess-smoothed plot of the similarity values along with the inflection point, if there are any. There is the option to search for an inflection point within a specified range. The package also has a function that will return the matrix components at a specified cutoff. 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>.

Matthew Cserhati

matrixcut

Determines Clustering Threshold Based on Similarity Values

cutoffplot function

<dl><dt>mx</dt>
<dd>a square sequence similarity matrix</dd>
<dt>lower_bound</dt>
<dd>lower bounds for calculating the inflection point in, default = 0</dd>
<dt>upper_bound</dt>
<dd>upper bounds for calculating the inflection point in, default = 1</dd></dl>

Arguments

Draws a Plot Showing the Number of Similarity Values as a Function
of the Cutoff Value. — cutoffplot

<dl>

<dt>mx</dt>
<dd>a square sequence similarity matrix</dd>


<dt>lower_bound</dt>
<dd>lower bounds for calculating the inflection point in, default = 0</dd>


<dt>upper_bound</dt>
<dd>upper bounds for calculating the inflection point in, default = 1</dd>

</dl>

cutoffplot: Draws a Plot Showing the Number of Similarity Values as a Function of the Cutoff Value.

Description

Value

Arguments

References

Examples