FactorViz provides an interactive visualization and reporting environment for exploring the results of the methylome decomposition experiments carried out by MeDeCom or similar deconvolution tools. It is the interpretation tool used in a recently published protocol to perform reference free deconvolution of complex DNA methylation data.
You can install the FactorViz through GitHub using devtools:
install.packages("devtools")
devtools::install_github("CompEpigen/FactorViz")
Installation has been tested on the following operating systems:
| Type | Distribution | Version | R-version | Installation successful | Protocol tested | Comments |
|---|---|---|---|---|---|---|
| Linux | Debian | Wheezy (7) | R-3.5.2 | Yes | Yes | |
| Linux | Debian | Wheezy (7) | R-3.6.0 | Yes | Yes | |
| Linux | Debian | Jessie (8) | R-3.5.3 | Yes | Yes (reduced) | |
| Linux | Debian | Jessie (8) | R-3.6.1 | Yes | No | |
| Linux | Debian | Jessie (8) | R-4.0 | Yes | No | |
| Linux | Debian | Buster (10) | R-3.5.2 | Yes | Yes (reduced) | |
| Linux | Fedora | 28 | R-3.5.3 | Yes | No | |
| Linux | Fedora | 31 | R-3.6.1 | No | Yes (reduced) | `igraph' dependency fails to install |
| Linux | CentOS | 8.0 | R-3.5.2 | Yes | Yes (reduced) | |
| Linux | CentOS | 8.0 | R-3.6.1 | Yes | Yes (reduced) | |
| Linux | Ubuntu | 19 | R-3.6.1 | Yes | Yes (reduced) | |
| MacOS | Mojave | R-3.5.1 | Yes | Yes (reduced) | binary release used | |
| MacOS | Catalina | R-3.6.0 | Yes | Yes (reduced) | ||
| Windows | 10 | Pro | R-3.6.1 | No | Yes (reduced) | Use docker image https://hub.docker.com/r/mscherer/medecom |
| Windows | 7 | Pro | R-3.6.1 | No | No | Docker is not available for Windows 7 |
You can start FactorViz by using startFactorViz() command, and then specify the output from DecompPipeline.
A more detailed introduction into FactorViz can be found in the package vignette.
FactorViz depends on MeDeCom and is thoroughly tested with outputs from DecompPipeline.