structure_plot: STRUCTURE Barplot

In mapmixture: Spatial Visualisation of Admixture on a Projected Map

STRUCTURE Barplot

Description

Plot a traditional STRUCTURE barplot or a facet barplot from individual admixture proportions.

Usage

structure_plot(
  admixture_df,
  type = "structure",
  cluster_cols = NULL,
  cluster_names = NULL,
  legend = "none",
  labels = "site",
  flip_axis = FALSE,
  ylabel = "Proportion",
  site_dividers = TRUE,
  divider_width = 1,
  divider_col = "white",
  divider_type = "dashed",
  site_order = NULL,
  display_site_labels = TRUE,
  site_labels_size = 2,
  site_labels_x = 0,
  site_labels_y = -0.025,
  site_labels_angle = 0,
  site_ticks = TRUE,
  site_ticks_size = -0.01,
  facet_col = NULL,
  facet_row = NULL
)

Arguments

admixture_df	data.frame or tibble containing admixture data (see examples).
type	show a traditional STRUCTURE barplot ("structure") or a facet barplot ("facet").
cluster_cols	character vector of colours the same length as the number of clusters. If NULL, a blue-green palette is used.
cluster_names	character vector of names the same length as the number of clusters. If NULL, the cluster column names are used.
legend	add legend at position ("none", "top", "right", "bottom" or "left"). Default is to hide legend.
labels	show labels at the site level or the individual level ("site" or "individual").
flip_axis	flip the axes so that the plot is vertical (TRUE or FALSE). Default is FALSE (horizontal barplot).
ylabel	string for y label.
site_dividers	add dotted lines that divide sites (TRUE or FALSE).
divider_width	width of site divider lines.
divider_col	colour of site divider lines.
divider_type	linetype of site divider line.
site_order	character vector of site labels used to customise the order of sites. If NULL, sites are ordered alphabetically.
display_site_labels	display site labels (TRUE or FALSE).
site_labels_size	numeric value for site label size.
site_labels_x	numeric value for site label horizontal position.
site_labels_y	numeric value for site label vertical position.
site_labels_angle	numeric value for rotating angle of site label.
site_ticks	show ticks when labels = "site".
site_ticks_size	numeric value for site tick size.
facet_col	number of columns to display for facet barplot.
facet_row	number of rows to display for facet barplot.

Value

A ggplot object.

Examples

# Admixture Format 1
file <- system.file("extdata", "admixture1.csv", package = "mapmixture")
admixture1 <- read.csv(file)

structure_plot(admixture1, type = "structure")
structure_plot(admixture1, type = "facet", facet_col = 5)

mapmixture documentation built on April 3, 2025, 7:45 p.m.