Piechart_map {PopGenHelpR}

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
)

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.

Value

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

Author(s)

Keaka Farleigh

Examples

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)