phylogeny tree labels not visible

[marianajeeb8]

Hello,

I am trying to build a gene presence absence matrix along with phylogeny tree using the provided code:

plot_tree_pa(tree = tree, pa = pa, genes = variable_genes, label_genes = FALSE, cols = "black")

Although I successfully obtained the final plot, I am concerned that the tip labels are not displaying, making it difficult to identify which samples contain unique genes. I am unsure whether this issue is due to overlapping and have not figured out how to adjust the tree's scale.

I would appreciate your help with this.

Also, thank you for providing this package for pangenome output visualization.

Maria

[gtonkinhill]

Hi Maria,

Sorry for the slow response. I've just pushed an update that should allow you to plot the tip names. After installing the latest version, you will need to specify label_tips=TRUE as a parameter in the updated function.