plot_graph: Plot an admixture graph

In uqrmaie1/admixtools: Inferring demographic history from genetic data

Plot an admixture graph

Description

Plot an admixture graph

Usage

plot_graph(
  graph,
  fix = NULL,
  title = "",
  color = TRUE,
  textsize = 2.5,
  highlight_unidentifiable = FALSE,
  pos = NULL,
  dates = NULL,
  neff = NULL,
  scale_y = FALSE,
  hide_weights = FALSE
)

Arguments

graph	An admixture graph. If it's an edge list with a label column, those values will be displayed on the edges
fix	If TRUE, there will be an attempt to rearrange the nodes to minimize the number of intersecting edges. This can take very long for large graphs. By default this is only done for graphs with fewer than 10 leaves.
title	A plot title
color	Plot it in color or greyscale
textsize	Size of edge and node labels
highlight_unidentifiable	Highlight unidentifiable edges in red. Can be slow for large graphs. See unidentifiable_edges.
pos	An optional data frame with node coordinates (columns node, x, y)
dates	An optional named vector with dates (in generations) for each node to plot dates on the y-axis (e.g., c('R'=1000, 'A'=0, 'B'=0)). If this option is supplied, the y-axis will display dates in generations.
neff	An optional named vector with effective population sizes for each population (e.g., c('R'=100, 'A'=100, 'B'=100)). If this option is supplied, the effective population size of each population will be shown next to the corresponding edge.
scale_y	If TRUE, scale the y-axis according to dates vector. The default is FALSE.
hide_weights	A boolean value specifying if the drift values on the edges will be hidden. The default is FALSE.

Value

A ggplot object

Examples

plot_graph(example_graph)

# Plot a random simulation output. Show dates and population sizes on the plot
out = random_sim(nleaf=5, nadmix=1)
plot_graph(out$edges, dates=out$dates, neff=out$neff)

uqrmaie1/admixtools documentation built on Nov. 3, 2024, 12:56 a.m.