plot_cladogram input file error?

[milanvarsadiya]

Hello,

I have been trying to create cladogram with plot_caldogram.py function but every time I run that command I'm getting an error saying that input-output files are not recognized. What should be the input file to run this function?

thank you

[twbattaglia]

Hi,

If you'd like to use plot_cladogram.py separate from the main command, you will need to specify one of the files within the run_lefse/ folder. The command would look something like this:

plot_cladogram.py \ 
output_folder/lefse_output/run_lefse/timepoint1.txt \
output_folder/lefse_output/run_lefse/timepoint1_cladogram.png \
--format png

[milanvarsadiya]

Hi,
Thank you for a prompt reply, I eventually figured it out myself. One more question regarding koeken.py function, why is not possible to use this function without splitting (-sp) mapping? It seems that I have to provide three column in the mapping file, without it, it will not work. Is it possible to use koeken.py without providing -sp function? It is really helpful function and I would like to use it more often.

[milanvarsadiya]

Hello,

While using koeken.py function I'm having some problems recently. Whenever I try to split the categorical variable (for instance, -cl horizon (different types) -sp Site (only one site)) I got this error message
rpy2.rinterface.RRuntimeError: Error in (function (cl, name, valueClass) :
‘xtrans’ is not a slot in class “NULL”

Can anybody help me to understand this error? I tried to dig on the internet but no success yet.