plot.pcoa.aggregate: Draw the aggregation plot for allelic differentiation

In HierDpart: Partitioning Hierarchical Diversity and Differentiation Across Metrics and Scales, from Genes to Ecosystems

Description

Ordination plot of the allelic differentiation. Draw the aggregation groups according to the hierarchical level.

Usage

plot_pcoa_aggregate(f, ncode, level, label = TRUE)

Arguments

f	Input files, genepop format
ncode	Genotype coding type
level	Hierarchical level (group)
label	Whether lable the aggregates or not, TRUE or FALSE

Details

PcoA ordination plot of the allelic differentiation between aggregates. If there is distinguishable difference between aggregates, the plot identifies the different aggregations

Author(s)

[e-mail]

Examples

f <- system.file('extdata',package='HierDpart')
infile <- file.path(f, "Island.gen")
region1=paste("region",rep(1,time=6))
region2=paste("region",rep(2,time=6))
region3=paste("region",rep(3,time=2))
region4=paste("region",rep(4,time=2))

level1=data.frame(matrix(data=0,nrow=16,ncol=1))
level1[1:6,1]=region1
level1[7:12,1]=region2
level1[13:14,1]=region3
level1[15:16,1]=region4
colnames(level1)=c("region")
plot_pcoa_aggregate(infile, ncode=3, level=level1$region, label = TRUE)

HierDpart documentation built on March 31, 2021, 5:09 p.m.