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,
  legend_pos = "right"
)

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 first two columns should indicate the sample name (first column) and the population that sample belongs to (second column). Other columns (i.e., latitude, longitude) can be present, but will not be used.
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: Character vector indicating the order to plot the populations in the population ancestry bar chart.
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.

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'))# }
#> [1] "All information needed is present, moving onto plotting."
#> [1] "Want to change the the text size, font, or any other formatting? See https://kfarleigh.github.io/PopGenHelpR/articles/PopGenHelpR_plotformatting.html for examples and help."