PopGenHelpR (version 1.4.0)

Piechart_map: Plot a map of ancestry pie charts.

Description

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
)

Value

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

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.

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)# }