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https://github.com/robjohnnoble/ggmuller
Create Muller Plots of Evolutionary Dynamics
https://github.com/robjohnnoble/ggmuller
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Create Muller Plots of Evolutionary Dynamics
- Host: GitHub
- URL: https://github.com/robjohnnoble/ggmuller
- Owner: robjohnnoble
- License: other
- Created: 2016-06-02T15:27:26.000Z (over 8 years ago)
- Default Branch: master
- Last Pushed: 2024-01-12T20:31:29.000Z (10 months ago)
- Last Synced: 2024-08-03T06:03:41.757Z (3 months ago)
- Language: R
- Size: 1.07 MB
- Stars: 64
- Watchers: 5
- Forks: 9
- Open Issues: 8
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
[](https://cran.r-project.org/package=ggmuller)
ggmuller
========
Create Muller Plots of Evolutionary Dynamics
### Installation
To install the [CRAN version](https://cran.r-project.org/package=ggmuller):
``` r
install.packages("ggmuller")
library(ggmuller)
```
To install the github version using devtools:
``` r
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:
``` r
# 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](https://cran.r-project.org/package=ggmuller/vignettes/ggmuller.html), 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](https://thesefewlines.wordpress.com/2016/08/20/how-to-ggmuller/).
### Version history
0.6.0: Use a much faster depth-first search algorithm.
0.5.6: Avoid loading or importing ape package, to avoid namespace conflict between ape and dplyr.
0.5.5: Optional removal of rare types is now much more efficient for large data sets.
0.5.4: Fix a rare bug; add tip labels to trees.
0.5.3: get_Muller_df now fills all columns when adding missing rows (issue #10); polygon edges now aren't drawn by default.
0.5.2: Can cope with the special case of only one genotype.
0.5.1: Can use brewer palettes.
0.5: Smoother plots from sparse data; time column can now be called "Time" instead of "Generation"; replace missing population sizes with zeroes.
0.4: Smoother plotting by default when genotypes suddenly grow from zero to large frequencies; new "start_positions" parameter can be used to override this default.
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 (2019). ggmuller: Create Muller Plots of Evolutionary Dynamics. R package version 0.5.3. 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 = {2019},
note = {R package version 0.5.3},
url = {https://CRAN.R-project.org/package=ggmuller},
doi = 10.5281/zenodo.591304
}
Please amend the version number as appropriate.