This R package is a companion to the PanViz javascript visualization for functionally annotated pangenomes. While PanViz is fully self-contained once it is created, this package takes care of converting your pangenome data into a PanViz file.

PanVizGenerator supports generic pangenome notation in the form of presence/absence matrices (also known as pangenome matrices) as well as a direct link to the FindMyFriends class system to allow for direct creation of PanViz from your FindMyFriends analysis.

Usage

There are two general approaches to generating PanViz visualizations with PanVizGenerator. Either using the panviz() method or by summoning a shiny app using the PanVizGenerator() function.

Simple example with csv input:

csvFile <- system.file('extdata', 'exampleData.csv', 
                       package = 'PanVizGenerator')
outputDir <- tempdir()

# Generate the visualization
panviz(csvFile, location = outputDir)

Or using FindMyFriends objects:

library(FindMyFriends)
# Load an example pangenome
pangenome <- .loadPgExample(withNeighborhoodSplit = TRUE)

# Add functional annotation from a Blast2GO analysis
annotation <- readAnnot(system.file('extdata', 
                                    'examplePG', 
                                    'example.annot', 
                                    package = 'FindMyFriends'))
pangenome <- addGroupInfo(pangenome, annotation, key = 'name')

# Generate the visualization
panviz(pangenome, location = outputDir)

Installation

This package is intended for future inclusion into the Bioconductor project. Until then it can be installed using devtools:

if (!require(devtools)) {
    install.packages('devtools')
    library(devtools)
}
install_github('thomasp85/PanVizGenerator')