structure_plot {mapmixture}

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,
  site_labels_size = 2,
  site_labels_x = 0,
  site_labels_y = -0.025,
  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.

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_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)