Mapmixture
R package and web app for spatial visualisation of admixture on a projected map
Install / Use
/learn @Tom-Jenkins/MapmixtureREADME
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mapmixture
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mapmixture is an R package and Shiny app that enables users to
visualise admixture as pie charts on a projected map. It also allows
users to visualise admixture as traditional structure barplots or facet
barplots.
Installation
mapmixture requires R (>= 4.2) to be
installed on your system. Click
here to download the
latest version of R for Windows.
Install the latest stable release from CRAN:
install.packages("mapmixture")
Install the latest development version from GitHub:
# install.packages("devtools")
devtools::install_github("Tom-Jenkins/mapmixture")
Reference
mapmixture() # main function
structure_plot() # plot traditional structure or facet barplot
scatter_plot() # plot PCA or DAPC results
launch_mapmixture() # launch mapmixture Shiny app
Citation
Jenkins TL (2024). <span class="smallcaps">mapmixture</span>: an R package and web app for spatial visualisation of admixture and population structure. Molecular Ecology Resources, 24: e13943. DOI: 10.1111/1755-0998.13943.
Examples
Basic usage of mapmixture
<details> <summary> Code </summary># Load package
library(mapmixture)
# Read in admixture file format 1
file <- system.file("extdata", "admixture1.csv", package = "mapmixture")
admixture1 <- read.csv(file)
# Read in coordinates file
file <- system.file("extdata", "coordinates.csv", package = "mapmixture")
coordinates <- read.csv(file)
# Run mapmixture
map1 <- mapmixture(admixture1, coordinates, crs = 3035)
# map1
Customised usage of mapmixture with a high resolution map
<details> <summary> Code </summary># Load packages
library(mapmixture)
library(rnaturalearthhires)
# Install rnaturalearthhires package using:
# install.packages("rnaturalearthhires", repos = "https://ropensci.r-universe.dev", type = "source")
# Read in admixture file format 1
file <- system.file("extdata", "admixture1.csv", package = "mapmixture")
admixture1 <- read.csv(file)
# Read in coordinates file
file <- system.file("extdata", "coordinates.csv", package = "mapmixture")
coordinates <- read.csv(file)
# Run mapmixture
map2 <- mapmixture(
admixture_df = admixture1,
coords_df = coordinates,
cluster_cols = c("#f1a340","#998ec3"),
cluster_names = c("Group A","Group B"),
crs = 3035,
basemap = rnaturalearthhires::countries10[, c("geometry")],
boundary = c(xmin=-15, xmax=16, ymin=40, ymax=62),
pie_size = 1,
pie_border = 0.3,
pie_border_col = "white",
pie_opacity = 1,
land_colour = "#d9d9d9",
sea_colour = "#deebf7",
expand = TRUE,
arrow = TRUE,
arrow_size = 1.5,
arrow_position = "bl",
scalebar = TRUE,
scalebar_size = 1.5,
scalebar_position = "tl",
plot_title = "Admixture Map",
plot_title_size = 12,
axis_title_size = 10,
axis_text_size = 8
)
# map2
Admixture map with single coloured circles
<details> <summary> Code </summary># Load package
library(mapmixture)
# Read in admixture file format 3
file <- system.file("extdata", "admixture3.csv", package = "mapmixture")
admixture3 <- read.csv(file)
# Read in coordinates file
file <- system.file("extdata", "coordinates.csv", package = "mapmixture")
coordinates <- read.csv(file)
# Run mapmixture
map3 <- mapmixture(admixture3, coordinates, crs = 3035)
# map3
Add additional geoms or theme options to mapmixture ggplot object
<details> <summary> Code </summary># Load packages
library(mapmixture)
library(ggplot2)
# Read in admixture file format 1
file <- system.file("extdata", "admixture1.csv", package = "mapmixture")
admixture1 <- read.csv(file)
# Read in coordinates file
file <- system.file("extdata", "coordinates.csv", package = "mapmixture")
coordinates <- read.csv(file)
# Run mapmixture
map4 <- mapmixture(
admixture_df = admixture1,
coords_df = coordinates,
cluster_cols = c("#f1a340","#998ec3"),
cluster_names = c("Ancestry 1","Ancestry 2"),
crs = 4326,
boundary = c(xmin=-15, xmax=16, ymin=40, ymax=62),
pie_size = 1,
)+
# Add additional label to the map
annotate("label",
x = -10,
y = 46.5,
label = "Atlantic Ocean",
size = 3,
)+
# Add additional text to the map
annotate("text",
x = 2.5,
y = 57,
label = "North Sea",
size = 3,
)+
# Adjust ggplot theme options
theme(
axis.title = element_text(size = 10),
axis.text = element_text(size = 8),
)+
# Adjust the size of the legend keys
guides(fill = guide_legend(override.aes = list(size = 5, alpha = 1)))
# map4
Combine admixture map and barplot ggplot objects into a single figure
<details> <summary> Code </summary># Load packages
library(mapmixture)
library(ggplot2)
library(gridExtra)
# Read in admixture file format 1
file <- system.file("extdata", "admixture1.csv", package = "mapmixture")
admixture1 <- read.csv(file)
# Read in coordinates file
file <- system.file("extdata", "coordinates.csv", package = "mapmixture")
coordinates <- read.csv(file)
# Run mapmixture
map5 <- mapmixture(
admixture_df = admixture1,
coords_df = coordinates,
cluster_cols = c("#f1a340","#998ec3"),
cluster_names = c("Ancestry 1","Ancestry 2"),
crs = 4326,
boundary = c(xmin=-20, xmax=20, ymin=40, ymax=62),
pie_size = 1.3,
)+
# Adjust theme options
theme(
legend.position = "top",
plot.margin = margin(l = 10, r = 10),
)+
# Adjust the size of the legend keys
guides(fill = guide_legend(override.aes = list(size = 5, alpha = 1)))
# Traditional structure barplot
structure_barplot <- structure_plot(
admixture_df = admixture1,
type = "structure",
cluster_cols = c("#f1a340","#998ec3"),
site_dividers = TRUE,
divider_width = 0.4,
site_order = c(
"Vigo","Ile de Re","Isles of Scilly","Mullet Peninsula",
"Shetland","Cromer","Helgoland","Flodevigen","Lysekil","Bergen"
),
labels = "site",
flip_axis = FALSE,
site_ticks_size = -0.05,
site_labels_y = -0.35,
site_labels_size = 2.2
)+
# Adjust theme options
theme(
axis.title.y = element_text(size = 8, hjust = 1),
axis.text.y = element_text(size = 5),
)
# Arrange plots
# grid.arrange(map5, structure_barplot, nrow = 2, heights = c(4,1))
# Load packages
library(mapmixture)
library(ggplot2)
library(gridExtra)
# Read in admixture file format 1
file <- system.file("extdata", "admixture1.csv", package = "mapmixture")
admixture1 <- read.csv(file)
# Read in coordinates file
file <- system.file("extdata", "coordinates.csv", package = "mapmixture")
coordinates <- read.csv(file)
# Run mapmixture
map6 <- mapmixture(
admixture_df = admixture1,
coords_df = coordinates,
cluster_cols = c("#f1a340","#998ec3"),
cluster_names = c("Ancestry 1","Ancestry 2"),
crs = 4326,
boundary = c(xmin=-20, xmax=20, ymin=40, ymax=62),
pie_size = 1.3,
)+
# Adjust theme options
theme(
legend.position = "top",
plot.margin = margin(l = 10, r = 10),
)+
# Adjust the size of the legend keys
guides(fill = guide_legend(override.aes = list(size = 5, alpha = 1)))
# Facet structure barplot
facet_barplot <- structure_plot(admixture1,
type = "facet",
cluster_cols = c("#f1a340","#998ec3"),
facet_col = 2,
ylabel = "Admixture proportions",
)+
theme(
axis.title.y = element_text(size = 10),
axis.text.y = element_text(size = 5),
strip.text = element_text(size = 6, vjust = 1, margin = margin(t=1.5, r=0, b=1.5, l=0)),
)
# Arrange plots
# grid.arrange(map6, facet_barplot, ncol = 2, widths = c(3,2))
Use a raster as the basemap
The raster (TIFF) used in the example below was downloaded from Natural
Earth
here.
You need to install the terra
package to use this feature. Currently, the basemap argument accepts a
SpatRaster or a sf object.
# Load packages
library(mapmixture)
library(terra)
# Create SpatRaster object
earth <- terra::rast("../NE1_50M_SR_W/NE1_50M_SR_W.tif")
# Read in admixture file format 1
file <- system.file("extdata", "admixture1.csv", package = "mapmixture")
admixture1 <- read.csv(file)
# Read in coordinates file
file <- system.file("extdata", "coordinates.csv", package = "mapmixture")
coordinates <- read.csv(file)
# Run mapmixture
map7 <- mapmixture(admixture1, coordinates, crs = 3035, basemap = earth)
# map7
Add pie charts to an existing map
The vector data (shapefile) used in t
