| Title: | Determines Clustering Threshold Based on Similarity Values |
|---|---|
| Description: | 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>. |
| Authors: | Matthew Cserhati [aut, cre]
|
| Maintainer: | Matthew Cserhati <[email protected]> |
| License: | GPL (>= 3) |
| Version: | 0.0.1 |
| Built: | 2024-08-23 06:18:57 UTC |
| Source: | CRAN |
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: [email protected] March 19, 2023
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 |
A plot showing the number of components as a function of the cutoff threshold.
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>
componentplot(xenarthra,0.75,0.9) componentplot(xenarthra)componentplot(xenarthra,0.75,0.9) componentplot(xenarthra)
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: [email protected] March 19, 2023
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 |
A plot showing the number of similarity values as a function of the cutoff threshold.
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>
cutoffplot(liliales,0.7,0.85) cutoffplot(liliales)cutoffplot(liliales,0.7,0.85) cutoffplot(liliales)
Chloroplast genome sequence similarity matrix for 163 Liliales species
lilialesliliales
## 'liliales' Chloroplast genome sequence similarity matrix for 163 Liliales species
The function takes a square sequence similarity matrix and calculates those independent components in which the sequence similarity between the members is greater than a specified value (between 0 and 1). The result provied by the function is a list of species with their component membership.
Version 0.0.1. Author: Dr. Matthew Cserhati Email: [email protected] March 19, 2023
mx |
a square sequence similarity matrix |
cut |
a given cutoff value to calculate components for, default value = -1 |
The inflection point: cutoff value for the optimal number of clusters
A list of the species together with their cluster membership.
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>
matrixcut(primates,0.8) matrixcut(primates)matrixcut(primates,0.8) matrixcut(primates)
Mitochondrial genome sequence similarity matrix for 31 primate species
primatesprimates
## 'primates' Mitochondrial genome sequence similarity matrix for 31 primate species
Mitochondrial genome sequence similarity matrix for 37 Xenarthra species
xenarthraxenarthra
## 'xenarthra' Mitochondrial genome sequence similarity matrix for 37 Xenarthra species