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KasperSkytte / ampvis2

Tools for visualising microbial community amplicon data
https://kasperskytte.github.io/ampvis2/
GNU General Public License v3.0
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Venn diagram of core OTUs #75

Closed apoosakkannu closed 4 years ago

apoosakkannu commented 5 years ago

Hi, I am trying to use ampvis2 (latest package) to plot venn diagram of core OTUs in my samples. But i am getting an following error, The code is 

amp_venn(
  ampvis2_physeq_clean_triatomine_nest_rarefy, 
  group_by = "T_cruzi", 
  cut_a = 0.1, 
  cut_f = 80,
  text_size = 5,
  normalise = TRUE, 
  detailed_output = FALSE
)

The error is "Factor OTU contains implicit NA, consider using `forcats::fct_explicit_na"

Could you give me solution to overcome this problem?

KasperSkytte commented 4 years ago

Hi there...

There are NA's in the taxonomy. You need to have a look at these and remove them in both $abund and $tax before continuing with anything.