| Version: | 0.0.1 |
| Date: | 2023-03-19 |
| Title: | Determines Clustering Threshold Based on Similarity Values |
| Maintainer: | Matthew Cserhati <csmatyi@protonmail.com> |
| 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. |
| License: | GPL (≥ 3) |
| Encoding: | UTF-8 |
| LazyData: | true |
| RoxygenNote: | 7.2.3 |
| Imports: | igraph, stats, inflection |
| NeedsCompilation: | no |
| Packaged: | 2023-03-24 04:49:15 UTC; matth |
| Author: | Matthew Cserhati 
[aut, cre] |
| Depends: | R (≥ 3.5.0) |
| Repository: | CRAN |
| Date/Publication: | 2023-03-24 16:30:02 UTC |
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: csmatyi@protonmail.com 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)
Draws a Plot Showing the Number of Similarity Values as a Function of the Cutoff Value.
Description
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
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 similarity values 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
cutoffplot(liliales,0.7,0.85)
cutoffplot(liliales)
Chloroplast genome sequence similarity matrix for 163 Liliales species
Description
Chloroplast genome sequence similarity matrix for 163 Liliales species
Usage
liliales
Format
## 'liliales' Chloroplast genome sequence similarity matrix for 163 Liliales species
Calculates The Component Membership in a Sequence Similarity Matrix at a given Cutoff Value
Description
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: csmatyi@protonmail.com March 19, 2023
Arguments
mx |
a square sequence similarity matrix |
cut |
a given cutoff value to calculate components for, default value = -1 |
Value
The inflection point: cutoff value for the optimal number of clusters
A list of the species together with their cluster membership.
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
matrixcut(primates,0.8)
matrixcut(primates)
Mitochondrial genome sequence similarity matrix for 31 primate species
Description
Mitochondrial genome sequence similarity matrix for 31 primate species
Usage
primates
Format
## 'primates' Mitochondrial genome sequence similarity matrix for 31 primate species
Mitochondrial genome sequence similarity matrix for 37 Xenarthra species
Description
Mitochondrial genome sequence similarity matrix for 37 Xenarthra species
Usage
xenarthra
Format
## 'xenarthra' Mitochondrial genome sequence similarity matrix for 37 Xenarthra species