Create Muller Plots of Evolutionary Dynamics

Create plots that combine a phylogeny and frequency dynamics. Phylogenetic input can be a generic adjacency matrix or a tree of class "phylo". Inspired by similar plots in publications of the labs of RE Lenski and JE Barrick. Named for HJ Muller (who popularised such plots) and H Wickham (whose code this package exploits).


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Create Muller Plots of Evolutionary Dynamics

To install the CRAN version:

install(ggmuller)
library(ggmuller)

To install the github version using devtools:

install.packages("devtools")
library(devtools)
  
install_github("robjohnnoble/ggmuller")
library(ggmuller)

Basic usage

The main functions in ggmuller are get_Muller_df and Muller_plot, which we can run on some data included in the package:

# reformat data ready for plotting:
Muller_df <- get_Muller_df(example_edges, example_pop_df)
 
# generate the plot:
Muller_plot(Muller_df)

How-to guides

The best place to start is the CRAN vignette, which includes an overview of features and some worked examples.

An older, slightly different set of instructions can be found in a blog post on Visualizing evolutionary dynamics with ggmuller.

Version history

0.3: Bug fixes; in particular, the "threshold" option is replaced by "cutoff" (genotypes whose abundance never exceeds "cutoff" are removed, whereas previously genotypes whose abundance never exceeded twice "threshold" were removed).

0.2.2: Bug fixes and deprecation of superfluous options.

0.2.1: Correct mistake in calculating population sizes for Muller_pop_plot.

0.2.0: New function Muller_pop_plot shows variation in population size as well as frequency (also known as a fish plot).

0.1.3: Compatibility with dplyr version 0.7.2; add option for smoother plotting of genotype emergence points.

0.1.2: Better plotting of the points at which genotypes emerge.

0.1.1: Essential update for compatibility with ggplot2 version 2.2.0.

0.1.0: First release.

Citation

To cite ggmuller in publications please use

Robert Noble (2017). ggmuller: Create Muller Plots of Evolutionary Dynamics. R package version 0.3. doi:10.5281/zenodo.591304 https://CRAN.R-project.org/package=ggmuller

A BibTeX entry for LaTeX users is

@Manual{,
title = {ggmuller: Create Muller Plots of Evolutionary Dynamics},
author = {Robert Noble},
year = {2017},
note = {R package version 0.3},
url = {https://CRAN.R-project.org/package=ggmuller},
doi = 10.5281/zenodo.591304
}

Please amend the version number as appropriate.

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Reference manual

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install.packages("ggmuller")

0.5.1 by Robert Noble, 7 days ago


Browse source code at https://github.com/cran/ggmuller


Authors: Robert Noble [aut, cre] (<https://orcid.org/0000-0002-8057-4252>)


Documentation:   PDF Manual  


MIT + file LICENSE license


Imports dplyr, ggplot2, ape

Suggests RColorBrewer, knitr, rmarkdown


See at CRAN