Package: ggmuller 0.6.0

ggmuller: 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).

Authors:Robert Noble [aut, cre]

ggmuller_0.6.0.tar.gz
ggmuller_0.6.0.zip(r-4.5)ggmuller_0.6.0.zip(r-4.4)ggmuller_0.6.0.zip(r-4.3)
ggmuller_0.6.0.tgz(r-4.4-any)ggmuller_0.6.0.tgz(r-4.3-any)
ggmuller_0.6.0.tar.gz(r-4.5-noble)ggmuller_0.6.0.tar.gz(r-4.4-noble)
ggmuller_0.6.0.tgz(r-4.4-emscripten)ggmuller_0.6.0.tgz(r-4.3-emscripten)
ggmuller.pdf |ggmuller.html✨
ggmuller/json (API)

# Install 'ggmuller' in R:

install.packages('ggmuller', repos = c('https://robjohnnoble.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/robjohnnoble/ggmuller/issues

Datasets:

example_df - Example dataframe
example_edges - Example adjacency matrix
example_pop_df - Example population dataframe

On CRAN:

7.28 score 64 stars 50 scripts 345 downloads 4 mentions 18 exports 34 dependencies

Last updated 1 years agofrom:25fd20b278. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 11 2024
R-4.5-win	OK	Nov 11 2024
R-4.5-linux	OK	Nov 11 2024
R-4.4-win	OK	Nov 11 2024
R-4.4-mac	OK	Nov 11 2024
R-4.3-win	OK	Nov 11 2024
R-4.3-mac	OK	Nov 11 2024

Exports:add_empty_pop add_root_row add_start_points adj_matrix_to_tree branch_singles find_start_node get_Adj get_edges get_Muller_df get_population_df move_down move_right move_up Muller_plot Muller_pop_plot path_vector path_vector_new reorder_by_vector

Dependencies:ape cli colorspace digest dplyr fansi farver generics ggplot2 glue gtable isoband labeling lattice lifecycle magrittr MASS Matrix mgcv munsell nlme pillar pkgconfig R6 RColorBrewer Rcpp rlang scales tibble tidyselect utf8 vctrs viridisLite withr

Introduction to ggmuller

Rendered fromggmuller.Rmdusingknitr::rmarkdownon Nov 11 2024.

Last update: 2023-09-18
Started: 2017-09-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Modify a dataframe to enable plotting of populations instead of frequencies	add_empty_pop
Add a row to the edges list to represent the root node (if not already present).	add_root_row
Add rows to a population dataframe to ensure genotype starting points are plotted correctly	add_start_points
Create a tree object of class "phylo" from an adjacency matrix	adj_matrix_to_tree
Add branches of length zero to get rid of single nodes in an adjacency matrix	branch_singles
Example dataframe	example_df
Example adjacency matrix	example_edges
Example population dataframe	example_pop_df
Move to top of adjacency matrix	find_start_node
Get adjacency list of a tree.	get_Adj
Extract an adjacency matrix from a larger data frame	get_edges
Create a data frame from which to create a Muller plot	get_Muller_df
Extract population data from a larger data frame	get_population_df
Move to daughter in adjacency matrix	move_down
Move to sibling in adjacency matrix	move_right
Move to parent in adjacency matrix	move_up
Draw a Muller plot of frequencies using ggplot2	Muller_plot
Draw a Muller plot of population sizes using ggplot2	Muller_pop_plot
Record a path through all nodes of an adjacency matrix	path_vector
Faster way to record a path through all nodes of an adjacency matrix	path_vector_new
Reorder a Muller plot dataframe by a vector	reorder_by_vector