LEFSE Plot

[Amir alipour yengejeh]

Hello all,

I am a new user of Lefse, and I have got this group very wonderful.

I am using LEfSe on Google Colab with Python 2.7 using the following commands:

!wget https://repo.anaconda.com/archive/Anaconda3-5.2.0-Linux-x86_64.sh && bash Anaconda3-5.2.0-Linux-x86_64.sh -bfp /usr/local

!conda install -c biobakery lefse 

import sys

sys.path.append('/usr/local/lib/python3.6/site-packages'

!format_input.py hmp_aerobiosis_small.txt hmp_aerobiosis_small.in -c 1 -s 2 -u 3 -o 1000000 

!run_lefse.py hmp_aerobiosis_small.in hmp_aerobiosis_small.res 

!plot_res.py hmp_aerobiosis_small.res hmp_aerobiosis_small.png

Everything is working, but there are some issues. The first problem is in LEfSe's plot such that it is drawing LDA scores' vertical lines with solid lines instead of dashed ones (standard format). Here are example of the image from the Tutorial (left) and what I am seeing (right). Secondly, is there any parameter for the following command to modify the view of plot such it would be more readable or not?

!plot_res.py hmp_aerobiosis_small.res hmp_aerobiosis_small.png

Finally, how can Iset the parameter such as p-values in the following commend to generate LDA score for all features without missing value, is it possible?

!run_lefse.py hmp_aerobiosis_small.in hmp_aerobiosis_small.res -a 1 -w 1 -l 0

Sincerely,

Amir.