Dendogram construction

[Martin Boys]

Dear Kamvar

Is there any possible way for me to bypass this error which I encountered when trying to plot a dendrogram. My dataset consists of 55 individuals, 10 loci, 3 populations and 1 stratum. Kindly see below the scripts and the outputs in bold which have led to the eventual error. Thank you in advance for your time and assistance.  

###GENETIC DISTANCE###

>library(poppr)

>library(ape)

>library(magrittr)

>martin25

This is a genclone object

-------------------------

Genotype information:

 

    4 original multilocus genotypes

   55 haploid individuals

   10 codominant loci

 

Population information:

 

    1 stratum - Pop

    3 populations defined - Hybrid, Heirloom, Grape

>set.seed(30)

>ten_samples<-sample(nInd(martin25),30)

>mic100<-martin25[ten_samples]

>(micdisc<-provesti.dist(mic100))

>theTree<-micdisc%>%nj()%>%ladderize()

>plot(theTree)

>add.scale.bar(length = 0.5)

>NJT1 <- last_plot()

###Bootstrap loci###

>set.seed(999)

>aboot(mic10, dist = provesti.dist, sample = 55, tree = "nj", cutoff = 50, quiet = TRUE)

Phylogenetic tree with 20 tips and 18 internal nodes.

Tip labels:

  T-69, T-77, T-2, T-63, T-46, T-58, ...

Node labels:

  NA, NA, NA, NA, NA, NA, ...

Unrooted; includes branch lengths.

Warning message:

In aboot(mic10, dist = provesti.dist, sample = 55, tree = "nj",  :

Some branch lengths of the tree are negative. Normalizing branches according to Kuhner and Felsenstein (1994)

>strata(martin25)<-data.frame(other(martin25))

Error: Number of rows in data frame not equal to number of individuals in object.

[Zhian Kamvar]

Hi Martin,

Before you post, check carefully the lines of code you are submitting. When you make an assignment, try printing the output and ask yourself "does this give me what I think it is giving me?
You are trying to set the strata from data.frame(other(martin25)). What is in `other(martin25)`? Likely, there is nothing there.
Read https://grunwaldlab.github.io/Population_Genetics_in_R/Population_Strata.html and see if that clears up the question about strata.

Best,

Zhian

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