Plot_ancestry {PopGenHelpR} | R Documentation |
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.
Description
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
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)