after run_lefse, plot_cladogram error

[LeeJH5120]

Using the Phyloseq object, after run_lefse, plot_ef_bar was normally derived.

However, plot_cladogram or microbiomeMarker::plot_cladogram
causes the following problem:

command
microbiomeMarker::plot_cladogram(phyloseq_df_run_lefse, color = c(A="steelblue",B="orange",C="darkgray",D="red",E="pink"))

"Error in if (n <= length(x)) { : missing value where TRUE/FALSE needed"

[SouravDutta79]

Hi,
I am also getting the same error.

I have used this commands -
mm_lefse <- run_lefse(
ps,
taxa_rank = "Genus",
norm = "rarefy",
group = "bodysite",
subgroup = "genotype"
)

plot_cladogram(mm_lefse, color = c("brown","blue","red","green"))

Error coming:
Error in if (n <= length(x)) { : missing value where TRUE/FALSE needed

Please help!

[BlueK77]

Hi, I am part of this club. I suffer the same error. In my opinion it seems to depend on taxa names as i manages to solve it filtering unassinged taxa. Unluckly I am facing the same problem again and i've already filtered taxa...I do not mind to share my left_out object if necesary

Thanx

[camcecc]

Same issue here after one year from yours, I agree with BlueK77 as I get the error only in the overall lefse output but not from the marker subset...

[zhanxw]

This issue is likely caused by invalid taxa names. For example, if the "Species" is unknown is the tax_table(ps), put NA there. This resolved our problem.