Error in (function (edges, n = max(edges), directed = TRUE) : At type_indexededgelist.c:117 : cannot create empty graph with negative number of vertices, Invalid value

[Leran10]

Hi,

I encountered this error when running taxatree_plots() function on my lm model. I checked around and it seems that the it is looking for numeric edge format but being provided with other format. But I'm not sure where to adjust my edge format to numeric? And I didn't encounter this error when I run this function in other datasets.

Thanks! Leran

[david-barnett]

Hi Leran, did you leave the ranks argument of taxatree_models as the default NULL ? I think there's a bug there I need to fix. If you did leave it as NULL, could you try naming the ranks you want to model in a vector c("phylum", "class", ... etc)

Please let me know if this helps?

(likewise for the previous issues where I have responded to you with follow-up questions, I would really appreciate it if you could reply again with any updates, it would be very helpful for me as I keep improving microViz 🙂 )

[Leran10]

Thanks for your reply, David, and I apologize for taking so long! Below is the code that I used:

CD.longitudinal.key <- taxatree_plotkey(
  data = CD.longitudinal.lm_models,
  taxon_renamer = function(x) stringr::str_remove(x, "[PFG]: "),
  rank == "Phylum" | rank == "Genus" & prevalence > 0.25,
  !grepl("Kingdom", taxon)
) + 
  scale_x_continuous(expand = expansion(mult = 0.2))

So as you can see I didn't leave rank parameter to NULL but set it to specific ranks.

BTW, microViz is a great tool and thanks for this excellent work.

Leran

[david-barnett]

improved robustness of taxatree plots in 0.10.2