Hello, I need assistance with plotting a phylogenetic tree for mitochondrial DNA. I have a VCF file with more than 10,000 samples, each with its own sub-haplogroup (in separate file). The variants and their genotypes were called using GATK best practices. I determined the haplogroups for all samples using HaploGrep software (command-line version). Now, I want to visualize these haplogroups in a phylogenetic tree. I have tried various methods in R without success. Here’s how I approached it: I used packages such as ape, factoextra, ggsci, and ggplot2 etc I created a data frame with sample IDs as row names and genotypes as columns.

Brief cmd used:

load data

vcf<-read.vcfR("~/ngs/20240224/20240319-MT/trees/chrMT.vcf.gz")

extract sample ID

sample_ids <- colnames(vcfgt)[-1]

Extract genotype data

genotype_data <- vcfgt genotype_df <- genotype_data[, -1]

My data frame looks like this.

dist_matrix <- dist(genotype_df)

Perform hierarchical clustering

hc <- hclust(dist_matrix)

Convert to dendrogram

dendrogram <- as.dendrogram(hc) hc <- hclust(distance_matrix, method = "average")

plot

fviz_dend(x=hc,cex = 0.4,lwd=0.09, h=7.5, k_colors = c("jco"), rect = TRUE, rect_border = "jco", type = "circular", rect_fill = TRUE).

Please see the attachment of the resulting plot.

The branches( tips) seem to be Individuals. But I wish to label the nodes and branches with haplogroups.

I would truly appreciate your assistance in successfully plotting this plot.

Thanks