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

Keaka Farleigh

Examples

# \donttest{
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'))# }