get_edges: Extract an adjacency matrix from a larger data frame

In ggmuller: Create Muller Plots of Evolutionary Dynamics

Extract an adjacency matrix from a larger data frame

Description

Extract an adjacency matrix from a larger data frame

Usage

get_edges(df, generation = NA)

Arguments

df	Dataframe inclduing column names "Identity", "Parent", and either "Generation" or "Time"
generation	Numeric value of Generation (or Time) at which to determine the adjacency matrix (defaults to final time point)

Value

A dataframe comprising the adjacency matrix.

Author(s)

Rob Noble, [e-mail]

See Also

get_population_df

Examples

## Not run: 
edges <- get_edges(example_df)

# extract the adjacency matrix from the data frame:
pop_df <- get_population_df(example_df)

# create data frame for plot:
Muller_df <- get_Muller_df(edges, pop_df)

require(RColorBrewer) # for the palette

# draw plot:
num_cols <- length(unique(Muller_df$RelativeFitness)) + 1
Muller_df$RelativeFitness <- as.factor(Muller_df$RelativeFitness)
Muller_plot(Muller_df, colour_by = "RelativeFitness", 
            palette = rev(colorRampPalette(brewer.pal(9, "YlOrRd"))(num_cols)), 
            add_legend = TRUE)

## End(Not run)

ggmuller documentation built on Feb. 16, 2023, 7:42 p.m.