In kevbobli224/EpiGPlot: Visualization of epigenetic factors

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EpiGPlot

The goal of EpiGPlot is to plot epigenetic genes expression values into interpretable data. Main function plotEpigeneticEV allows for specific linear regression model visualization on user-specified sample classes.

Installation

You can install the development version of EpiGPlot like so:

require("devtools")
install_github("kevbobli224/EpiGPlot", build_vignettes = TRUE)
library("EpiGPlot")

To run the Shiny App:

EpiGPlot::runEpiGPlot()

Description/Overview

The package's purpose is to plot and visualize epigenetic factor data sets into simple and interpretable visualization plots.

Established epigenetic factor databases do not have visualization methods for gene data sets, this package aims to fill and addresses the visualization gap by plotting expression values of given gene set against a range of quantile genes.

EpiGPlot contains 4 exported functions for users: For plotting purposes and graphing linear regression models: plotEpigeneticEV

For customizing plotting layouts and specifications: layoutEpigeneticEV

For parsing .csv or loading .rda data for a certain gene and their expression values amongst other genes: parseEpigeneticData, loadEpigeneticData

Refer to vignette or manual for detailed usage of the provided functions.

Function examples in the manuals are only given to the exported functions. Non-exported functions will not have an example.

An overview of the package is illustrated below.

A Shiny application could be run for the ease of visualization. To run the Shiny App:

EpiGPlot::runEpiGPlot()

An illustration of a shiny app:

Details

For more details, see vignette

To list all functions available in the package:

ls("package:EpiGPlot")

To list all provided data sets in the package:

data(package="EpiGPlot")

A package tree structure is provided as below:

- EpiGPlot
  |- EpiGPlot.Rproj
  |- DESCRIPTION
  |- NAMESPACE
  |- LICENSE
  |- README
  |- data
    |- NO66_HUMAN.rda
  |- inst
    |- CITATION
    |- shiny-scripts
      |- app.R
    |- extdata
      |- expression.csv
      |- Plot1_default.png
      |- Plot2_spec_class.png
      |- Plot3_spec_lr.png
      |- overview.png
      |- overview_shiny.PNG
  |- man
    |- getColourMattrix.Rd
    |- getGeneClassColour.Rd
    |- layoutEpigeneticEV.Rd
    |- loadEpigeneticData.Rd
    |- NO66_HUMAN.Rd
    |- parseEpigeneticData.Rd
    |- plotEpigeneticEV.Rd
    |- pScaleRange.Rd
  |- R
    |- data.R
    |- epiGPlotFunctions.R
    |- runEpiGPlot.R
  |- vignettes
    |- EpiGPlot.Rmd
    |- EpiGPlot.R
    |- EpiGPlot.html
  |- tests
    |- testthat.R
    |- testthat
      |- test-epiGPlotFunctions.R

Or, refer to vignette for more details.

Contributions

The plotEpigeneticEV function uses ggplot and ggrepel packages to perform plotting functions, as well as grDevices package for the layoutEpigeneticEV function to parse and validate hexadecimal colour strings. shiny is utilized for interactive web application for ease of package interaction.

References for Package

• Medvedeva, Y. A., Lennartsson, A., Ehsani, R., Kulakovskiy, I. V., Vorontsov, I. E., Panahandeh, P., Khimulya, G., Kasukawa, T., & Drabløs, F. (2015). Epifactors: A comprehensive database of human epigenetic factors and complexes. Database, 2015.

Acknowledgement

This package was developed as part of an assessment for 2021 BCB410H: Applied Bioinfor-matics, University of Toronto, Toronto, CANADA.

Tutorials

For tutorials and plot interpretation, refer to the vignette:

browseVignettes("EpiGPlot")

Sample Outputs

knitr::include_graphics(c("inst/extdata/Plot1_default.png","inst/extdata/Plot2_spec_class.png", "inst/extdata/Plot3_spec_lr.png"))

kevbobli224/EpiGPlot documentation built on Dec. 21, 2021, 6:35 a.m.