Problems finding my organism in pathview

[hilariodc]

Hi! I´m trying to do some analysis using the tool pathway in Rstudio, but I have a problem. When I search my micoorganism in kegg it looks like there´s no problem:

#search_kegg_organism('psav', by='kegg_code')
search_kegg_organism(str="Pseudomonas savastanoi pv. savastanoi", by="scientific_name", use_internal_data=FALSE)
kegg_code scientific_name common_name
1726 psav Pseudomonas savastanoi pv. savastanoi Pseudomonas savastanoi pv. savastanoi

But when I try to look for my microorganism in the Pathview database it appears this error:

pv.out.bs <- pathview(gene.data = geneList,

•                   gene.idtype="kegg", 
  

•                   pathway.id = "03010", 
  

•                   species = "psav", 
  

•                   out.suffix = "kegg")
  

Note: Unknown species 'psav'!
Error in kegg.species.code(species, na.rm = T, code.only = FALSE) :
All species are invalid!

Do you know where is the problem? Thank you in advance

[chenchen-eng]

Hello, I also had the same problem, please did you solve it

[raw937]

I think we can help you here.

Unlikely your species isn't present.

We have a new tool from my group called metacereberus that can get you your KO annotations.
It also as scripts that call pathview that is integrated.
https://github.com/raw-lab/MetaCerberus