Ancestry_barchart {PopGenHelpR}

Plot an ancestry matrix for individuals and(or) populations.

Description

Plot an ancestry matrix for individuals and(or) populations.

Usage

Ancestry_barchart(
  anc.mat,
  pops,
  K,
  plot.type = "all",
  col,
  ind.order = NULL,
  pop.order = 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.

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 for both the individuals and populations.

col

Character vector indicating the colors you wish to use for plotting.

ind.order

Character vector indicating the order to plot the individuals in the individual ancestry bar chart.

pop.order

Chracter vector indicating the order to plot the populations in the population ancesyry bar chart.

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 <- Ancestry_barchart(anc.mat = Qmat, pops = Loc, K = 5,
plot.type = 'all',col = c('#d73027', '#fc8d59', '#e0f3f8', '#91bfdb', '#4575b4'))