mpqDist is an R package for computing a family of phylogenetically-informed distances and making a interactive plots based on them. The MPQ distances are a family of distance with a continuous tuning parameter which controls the extent to which the distance is influenced by basal vs. terminal phylogenetic structure. The package allows the user to give a template for a plot which will be filled in with the full spectrum of tuning parameters. Given a template, the package uses plotly to create an interactive plot that allows the user to scan through versions of the plot filled in with all the members of the family.
Installation
The package can be installed using devtools::install_github('jfukuyama/mpqDist').
It requires the bioconductor package phyloseq, so if you get an error that says that phyloseq is not available, you need to install it from bioconductor using
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("phyloseq")Vignettes
Vignettes showing simulations and real data analysis are available in the vignettes folder. Compiled html documents from those vignettes are available in docs. At this time, the html documents need to be downloaded to your machine (github doesn’t display them nicely), but they are self-contained and once they are downloaded you can see all the figures and the interactive plots that are created in the vignettes.
You can also install the package and run vignette(package = "mpqDist") to see the vignettes. For example, one of the vignettes is called gentry, which can be accessed using vignette("gentry", package = "mpqDist").