| Type: | Package |
| Title: | Exploiting Local Structures to Improve Network-Based Analysis of Biological Data |
| Version: | 0.99.0 |
| Depends: | R (≥ 3.4.0) |
| Imports: | methods, utils, RANN, Matrix, RSpectra |
| Suggests: | scatterplot3d, knitr, rmarkdown, testthat |
| Description: | Compared with the similar graph embedding method such as Laplacian Eigenmaps, 'Vicus' can exploit more local structures of graph data. For the details of the methods, see the reference section of 'GitHub' README.md https://github.com/rikenbit/Vicus. |
| License: | MIT + file LICENSE |
| URL: | https://github.com/rikenbit/Vicus |
| VignetteBuilder: | knitr |
| NeedsCompilation: | no |
| Packaged: | 2023-03-23 10:25:26 UTC; koki |
| Author: | Koki Tsuyuzaki [aut, cre] |
| Maintainer: | Koki Tsuyuzaki <k.t.the-answer@hotmail.co.jp> |
| Repository: | CRAN |
| Date/Publication: | 2023-03-23 19:32:04 UTC |
Exploiting Local Structures to Improve Network-Based Analysis of Biological Data
Description
Compared with the similar graph embedding method such as Laplacian Eigenmaps, 'Vicus' can exploit more local structures of graph data. For the details of the methods, see the reference section of 'GitHub' README.md <https://github.com/rikenbit/Vicus>.
Details
The DESCRIPTION file:
| Package: | Vicus |
| Type: | Package |
| Title: | Exploiting Local Structures to Improve Network-Based Analysis of Biological Data |
| Version: | 0.99.0 |
| Authors@R: | c(person("Koki", "Tsuyuzaki", role = c("aut", "cre"), email = "k.t.the-answer@hotmail.co.jp")) |
| Depends: | R (>= 3.4.0) |
| Imports: | methods, utils, RANN, Matrix, RSpectra |
| Suggests: | scatterplot3d, knitr, rmarkdown, testthat |
| Description: | Compared with the similar graph embedding method such as Laplacian Eigenmaps, 'Vicus' can exploit more local structures of graph data. For the details of the methods, see the reference section of 'GitHub' README.md <https://github.com/rikenbit/Vicus>. |
| License: | MIT + file LICENSE |
| URL: | https://github.com/rikenbit/Vicus |
| VignetteBuilder: | knitr |
| Author: | Koki Tsuyuzaki [aut, cre] |
| Maintainer: | Koki Tsuyuzaki <k.t.the-answer@hotmail.co.jp> |
Index of help topics:
Vicus-package Exploiting Local Structures to Improve
Network-Based Analysis of Biological Data
embedding Graph Embedding
graphMatrix Graph Laplacian type matrix
Author(s)
NA
Maintainer: NA
References
Wang B, et al., (2017). Vicus: Exploiting local structures to improve network-based analysis of biological data. PLOS Computational Biology. 13(10), e1005621
See Also
Examples
ls("package:Vicus")
Graph Embedding
Description
Lower dimensions are estimated from the object returned from graphMatrix function.
Usage
embedding(obj)
Arguments
obj |
Object returned from graphMatrix function. |
Value
A matrix (n times k)
Author(s)
Koki Tsuyuzaki
See Also
Examples
X <- matrix(runif(10*20), nrow=10, ncol=20)
head(embedding(graphMatrix(X, K=2)))
Graph Laplacian type matrix
Description
A symmetric matrix is returned.
Usage
graphMatrix(X, algorithm=c("Vicus", "LEM", "HLLE"),
K=10, alpha=0.9, ndim=2)
Arguments
X |
A numeric matrix (n times p). |
algorithm |
Algorithm to construct a graph matrix. Vicus matrix (Vicus), Graph Laplacian matrix (LEM), and Hessian Locally Linear Embedding matrix (HLLE) are available (Default: "Vicus"). |
K |
The number of neighborhoods to construct a graph matrix (Default: 10). |
alpha |
An optional parameter for Vicus (Default: 0.9). |
ndim |
The number of lower dimension to embed the graph (Default: 2). |
Value
M: A symmetric matrix (n times n). This matrix can be applied to embedding function. algorithm: algorithm parameter specified by argument ndim: ndim parameter specified by argument
Author(s)
Koki Tsuyuzaki
See Also
Examples
X <- matrix(runif(10*20), nrow=10, ncol=20)
str(graphMatrix(X, K=2), 2)