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WARNING! This function has been deprecated and is no longer supported. Please use the Ancestry_barchart and Piechart_map functions. Plot an ancestry matrix and map of ancestry pie charts.

Source: R/Plot_ancestry.R
Plot_ancestry.Rd

WARNING! This function has been deprecated and is no longer supported. Please use the Ancestry_barchart and Piechart_map functions. Plot an ancestry matrix and map of ancestry pie charts.

Usage

Plot_ancestry(
  anc.mat,
  pops,
  K,
  plot.type = "all",
  col,
  piesize = 0.35,
  Lat_buffer,
  Long_buffer
)

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.

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 barchart and 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.

Value

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

Examples

# \donttest{
data(Q_dat)
Qmat <- Q_dat[[1]]
rownames(Qmat) <- Qmat[,1]
Loc <- Q_dat[[2]]
Test_all <- Plot_ancestry(anc.mat = Qmat, pops = Loc, K = 5,
plot.type = 'all', col <- c('red', 'maroon', 'navy', 'cyan', 'blue'), piesize = 0.35,
Lat_buffer = 1, Long_buffer = 1)# }
#> Warning: The Plot_ancestry function has been deprecated as of PopGenHelpR v1.3.0 and will dissappear in v2.0.0. Please use the Piechart_map and Ancestry_barchart function(s) if you wish to plot ancestry maps or barcharts.