Plot a map of ancestry pie charts.

Usage

Piechart_map(
  anc.mat,
  pops,
  K,
  plot.type = "all",
  col,
  piesize = 0.35,
  Lat_buffer,
  Long_buffer,
  Latitude_col = NULL,
  Longitude_col = NULL,
  country_code = NULL,
  shapefile = NULL,
  legend_pos = "none",
  scale_bar = FALSE,
  north_arrow = FALSE,
  north_arrow_style = ggspatial::north_arrow_nautical(),
  north_arrow_position = NULL,
  shapefile_plot_position = NULL,
  shapefile_col = NULL,
  shapefile_outline_col = NULL,
  shp_outwidth = 1
)

Arguments

anc.mat: Data frame or character string that supplies the input data. If it is a character string, the file should be a csv. The first column should be the names of each sample/population, followed by the estimated contribution of each cluster to that individual/pop.
pops: Data frame or character string that supplies the input data. If it is a character string, the file should be a csv. The columns should be named Sample, containing the sample IDs; Population indicating the population assignment of the individual, population and sample names must be the same type (i.e., both numeric or both characters); Long, indicating the longitude of the sample; Lat, indicating the latitude of the sample. Alternatively, see the Longitude_col and Latitude_col arguments.
K: Numeric.The number of genetic clusters in your data set, please contact the package authors if you need help doing this.
plot.type: Character string. Options are all, individual, and population. All is default and recommended, this will plot a piechart map for both the individuals and populations.
col: Character vector indicating the colors you wish to use for plotting.
piesize: Numeric. The radius of the pie chart for ancestry mapping.
Lat_buffer: Numeric. A buffer to customize visualization.
Long_buffer: Numeric. A buffer to customize visualization.
Latitude_col: Numeric. The number of the column indicating the latitude for each sample. If this is not null, PopGenHelpR will use this column instead of looking for the Lat column.
Longitude_col: Numeric. The number of the column indicating the longitude for each sample. If this is not null, PopGenHelpR will use this column instead of looking for the Long column.
country_code: Character. A country code or vector of country codes from the R package geodata specifying the country that you want to plot administrative borders for (e.g, US states). You can determine the correct codes using geodata's country_codes function.
shapefile: Character. A file name, vector of file names of a shapefile(s) to plot on the map, or a spatvector object that is compatible with the R package terra. This should be used in conjunction with the shapefile_plot_position argument.
legend_pos: Character. The desired position of the legend. The default is "none", which removes the legend. Other options include "left", "right", "top" or "bottom". Please see the ggplot2 documentation for all of the legend placement options.
scale_bar: Boolean. Whether or not to add a scale bar. Note that maps with large areas or those that use unprojected spatial data (i.e., WGS 84) will generate a warning that the scale bar varies.
north_arrow: Boolean. Whether or not to add a north arrow.
north_arrow_style: Character. Which style of north arrow to add. See ggspatial documentation for more details.
north_arrow_position: Character. The position of the north arrow. See ggspatial documentation for more details.
shapefile_plot_position: Numeric. A number indicating which position to plot the shapefile in. The options are 1, which plots the shapefile on top of the base world map (under points and administrative boundaries), 2 which plots the shapefile on top of administrative boundaries (but under points), and 3, which plots the shapefile on top of everything.
shapefile_col: Character. A color or color vector indicating the color to fill the shapefile(s) with. Similar to group_col, shapefiles will be colored alphabetically.
shapefile_outline_col: Character. A color indicating the outline color of the shapefile.
shp_outwidth: Numeric. The width of the shapefile outline.

Value

A list containing your plots and the data frames used to generate the plots.

Author

Keaka Farleigh

Examples

# \donttest{
data(Q_dat)
Qmat <- Q_dat[[1]]
rownames(Qmat) <- Qmat[,1]
Loc <- Q_dat[[2]]
Test_all <- Piechart_map(anc.mat = Qmat, pops = Loc, K = 5,
plot.type = 'all', col = c('#d73027', '#fc8d59', '#e0f3f8', '#91bfdb', '#4575b4'), piesize = 0.35,
Lat_buffer = 1, Long_buffer = 1)# }