Package 'mapmixture'

Launch Shiny App

Description

Wrapper function used to start mapmixture interactive app.

App tested with the following package versions:

shiny v1.8.0, shinyFeedback v0.4.0, shinyjs v2.1.0, shinyWidgets 0.8.4, bslib 0.7.0, colourpicker 1.3.0, htmltools v0.5.8.1, waiter 0.2.5.

Usage

launch_mapmixture(...)

Arguments

...	additional arguments passed to shiny::runApp().

Value

No return value.

Examples

if (interactive()){
  launch_mapmixture(launch.browser = TRUE)
}

---

Plot Pie Charts on Map

Description

Plot admixture proportions as pie charts on a projected map. In data sets where there are multiple individuals per site, the function will calculate the mean average admixture proportion for each site.

Usage

mapmixture(
  admixture_df,
  coords_df,
  cluster_cols = NULL,
  cluster_names = NULL,
  boundary = NULL,
  crs = 4326,
  basemap = NULL,
  pie_size = 1,
  pie_border = 0.2,
  pie_border_col = "black",
  pie_opacity = 1,
  land_colour = "#d9d9d9",
  sea_colour = "#deebf7",
  expand = FALSE,
  arrow = TRUE,
  arrow_size = 1,
  arrow_position = "tl",
  scalebar = TRUE,
  scalebar_size = 1,
  scalebar_position = "tl",
  plot_title = "",
  plot_title_size = 12,
  axis_title_size = 10,
  axis_text_size = 8,
  basemap_border = TRUE,
  basemap_border_col = "black",
  basemap_border_lwd = 0.1
)

Arguments

admixture_df	data.frame or tibble containing admixture data (see examples).
coords_df	data.frame or tibble containing coordinates data (see examples).
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 clusters are named cluster01, cluster02, ..., clusterN.
boundary	named numeric vector defining the map bounding. e.g. c(xmin=-15, xmax=15, ymin=30, ymax=50). If NULL, a default bounding box is calculated.
crs	coordinate reference system. Default is the WGS 84 - World Geodetic System 1984 (EPSG:4326). See ?sf::st_crs for details.
basemap	SpatRaster or sf object to use as the basemap. A SpatRaster object can be created from a file using the terra::rast() function. A sf object can be created from a file using the sf::st_read() function. If NULL, world country boundaries are used.
pie_size	vector of numeric values of zero or greater. Can be a single value or a vector the same length as the number of sites.
pie_border	numeric value of zero or greater.
pie_border_col	string denoting colour of pie border.
pie_opacity	numeric value of zero to one.
land_colour	string defining the colour of land.
sea_colour	string defining the colour of sea.
expand	expand axes (TRUE or FALSE).
arrow	show arrow (TRUE or FALSE). Added using the ggspatial::annotation_north_arrow() function.
arrow_size	numeric value of zero or greater.
arrow_position	string defining the position of the arrow ("tl", "tr", "bl", "br").
scalebar	show scalebar (TRUE or FALSE). Added using the ggspatial::annotation_scale() function.
scalebar_size	numeric value of zero or greater.
scalebar_position	string defining the position of the scalebar ("tl", "tr", "bl", "br").
plot_title	string defining the main title of the plot.
plot_title_size	numeric value of zero or greater.
axis_title_size	numeric value of zero or greater.
axis_text_size	numeric value of zero or greater.
basemap_border	boolean denoting whether to show basemap polygon borders.
basemap_border_col	string defining colour of basemap polygon borders.
basemap_border_lwd	numeric value defining linewidth of basemap polygon borders.

Value

A ggplot object.

Examples

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

# Admixture Format 2
file <- system.file("extdata", "admixture2.csv", package = "mapmixture")
admixture2 <- read.csv(file)

# Admixture Format 3
file <- system.file("extdata", "admixture3.csv", package = "mapmixture")
admixture3 <- read.csv(file)

# Coordinates Format
file <- system.file("extdata", "coordinates.csv", package = "mapmixture")
coordinates <- read.csv(file)

# Plot using default parameters
mapmixture(admixture1, coordinates)

# Plot using the ETRS89-extended / LAEA Europe coordinate reference system
mapmixture(admixture1, coordinates, crs = 3035)

# Plot using custom parameters
mapmixture(
  admixture_df = admixture1,
  coords_df = coordinates,
  cluster_cols = c("#f1a340","#998ec3"),
  cluster_names = c("Group 1","Group 2"),
  crs = "+proj=merc +a=6378137 +b=6378137 +lat_ts=0 +lon_0=0 +x_0=0 +y_0=0 +units=m",
  boundary = c(xmin=-15, xmax=16, ymin=40, ymax=62),
  pie_size = 1.5,
  pie_border = 0.2,
  pie_opacity = 1,
  land_colour = "#d9d9d9",
  sea_colour = "#deebf7",
  expand = FALSE,
  arrow = TRUE,
  arrow_size = 1,
  arrow_position = "tl",
  scalebar = TRUE,
  scalebar_size = 1,
  scalebar_position = "tl",
  plot_title = "Mapmixture Figure",
  plot_title_size = 15,
  axis_title_size = 12,
  axis_text_size = 10
)

---

PCA or DAPC Scatter Plot

Description

Plot a scatter plot of PCA or DAPC results.

Usage

scatter_plot(
  dataframe,
  group_ids,
  other_group = NULL,
  type = "points",
  ...,
  labels = NULL,
  axes = c(1, 2),
  colours = NULL,
  centroids = TRUE,
  segments = TRUE,
  point_size = 3,
  point_type = 21,
  centroid_size = 3,
  hvline_type = "dotted",
  hvline_size = 0.5,
  hvline_colour = "black",
  xlab = "Axis",
  ylab = "Axis",
  percent = NULL,
  plot_title = ""
)

Arguments

dataframe	data.frame or tibble containing results from a PCA or DAPC (see examples).
group_ids	character vector of IDs representing the group each row belongs to. This is used to colour the scatter plot and (optionally) add centroids and segments. E.g. a vector of site names, a vector of biological categories such as male or female, etc.
other_group	secondary character vector of IDs defining how to colour the scatter plot. E.g. a vector of country names (see examples). If NULL, scatter plot is coloured by group_ids.
type	string defining whether to show points ("points"), labels ("labels"), or text ("text").
...	additional arguments passed to ggplot2::geom_point when type = "points", or to ggplot2::geom_label when type = "labels", or to ggplot2::geom_text when type = "text".
labels	character vector of IDs defining labels when type = "label" or type = "text". If NULL, row names are used (integers from 1:nrow(dataframe)).
axes	integer vector of length two defining which axes to plot.
colours	character vector of colours the same length as the number of groups defined in group_ids or other_group.
centroids	add centroids to plot (TRUE or FALSE).
segments	add segments to plot (TRUE or FALSE).
point_size	numeric value for point size.
point_type	numeric value for point type (shape).
centroid_size	numeric value for centroid label size.
hvline_type	integer or string defining linetype (1 or "dotted"). Input 0 for no horizontal and vertical lines.
hvline_size	integer defining linewidth.
hvline_colour	string defining line colour.
xlab	string defining x axis label.
ylab	string defining y axis label.
percent	numeric vector the same length as ncol(dataframe) defining the percentage of variance explained by each axis.
plot_title	string defining the main title of the plot.

Value

A ggplot object.

Examples

# Results from a Principal Components Analysis
file <- system.file("extdata", "pca_results.csv", package = "mapmixture")
pca_results <- read.csv(file)

# Define parameters
ind_names <- row.names(pca_results)
site_names <- rep(c("Pop1", "Pop2", "Pop3", "Pop4", "Pop5", "Pop6"), each = 100)
region_names <- rep(c("Region1", "Region2"), each = 300)
percent <- c(5.6, 4.5, 3.2, 2.0, 0.52)

# Scatter plot
scatter_plot(pca_results, site_names)

# Scatter plot with axes 1 and 3 and percent on axis labels
scatter_plot(pca_results, site_names, axes = c(1,3), percent = percent)

# Scatter plot with no centroids and segments
scatter_plot(pca_results, site_names, axes = c(1,2), percent = percent,
             centroids = FALSE, segments = FALSE)

# Scatter plot with custom colours and coloured by other_group
scatter_plot(pca_results, site_names, other_group = region_names,
             percent = percent, colours = c("#f1a340","#998ec3"))

# Scatter plot with individual labels
scatter_plot(pca_results, site_names, type = "labels",
             labels = rownames(pca_results))

# Scatter plot with individual text
scatter_plot(pca_results, site_names, type = "text",
             labels = rownames(pca_results))

---

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)

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