How to build pie charts in haploNet Haplotype Networks {pegas}
I am trying to use the haploNet {pegas} function to build a haplotype network, but I am having trouble setting equal haplotypes from different populations on the same pie. I can build a haplotype network with the following script:
x <- read.dna(file="x.fas",format="fasta")
h <- haplotype(x)
net <- haploNet(h)
plot(net)
I would like to set in the dnabin data the label of the original population of each taxon, so in the resulting network I could have pivot plots of different colors (from haplotypes from different populations). I would also like to remove the overlapping circles in the resulting haplotype network.
Thanks for any help!
Example:
> data(woodmouse)
> x <- woodmouse[sample(15, size = 110, replace = TRUE), ]
> h <- haplotype(x)
> net <- haploNet(h)
> plot(net, size=attr(net, "freq"), scale.ratio = 2, cex = 0.8)
This script is used to create a haplotype network using {pegas}. Large circles represent many more haplotypes of some kind. I would like to know how I could set the start of the haplotypes in the dnabin matrix so that they appear with different colors on the net.
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Ok, trying to understand the meaning of your example. It looks like you have a population of 15 people with 3 to 13 samples per population.
table(rownames(x))
# No0906S No0908S No0909S No0910S No0912S No0913S No1007S
# 10 8 6 3 3 7 6
# No1103S No1114S No1202S No1206S No1208S No304 No305
# 4 13 9 6 9 13 7
# No306
# 6
When you run haplotype(x)
, you get (unsurprisingly) 15 haplotypes, representing a 1: 1 mapping from population to haplotype. We can create a table showing the relationship between populations and haplotypes using
ind.hap<-with(
stack(setNames(attr(h, "index"), rownames(h))),
table(hap=ind, pop=rownames(x)[values])
)
ind.hap[1:10, 1:9] #print just a chunk
# pop
# hap No0906S No0908S No0909S No0910S No0912S No0913S No1007S No1103S No1114S
# I 0 0 0 0 0 0 0 0 0
# II 0 0 0 0 0 0 6 0 0
# III 0 0 0 0 0 0 0 4 0
# IV 10 0 0 0 0 0 0 0 0
# IX 0 0 0 0 0 0 0 0 0
# V 0 0 6 0 0 0 0 0 0
# VI 0 0 0 0 0 0 0 0 0
# VII 0 0 0 0 0 7 0 0 0
# VIII 0 0 0 0 0 0 0 0 13
# X 0 0 0 0 0 0 0 0 0
We can use this table while plotting to draw pic symbols on each of the nodes.
plot(net, size=attr(net, "freq"), scale.ratio = 2, cex = 0.8, pie=ind.hap)
legend(50,50, colnames(ind.hap), col=rainbow(ncol(ind.hap)), pch=20)
To show pie charts better, we can assign incorrect populations to each of the samples
wrong.pop<-rep(letters[1:5], each=22)
ind.hap2<-with(
stack(setNames(attr(h, "index"), rownames(h))),
table(hap=ind, pop=wrong.pop[values])
)
plot(net, size=attr(net, "freq"), scale.ratio = 2, cex = 0.8, pie=ind.hap2)
legend(50,50, colnames(ind.hap2), col=rainbow(ncol(ind.hap2)), pch=20)
Here you can see that we have more variety in each haplotype because we are mislabeled by the population with artificial names so they don't shrink so well.
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