LeFSE after Qiime2 for quantitative analysis (no subclass)


I’ve been working on the analysis of Qiime2 (qiime2-2021.2) results using LEfSe and I wasn’t able to use the command “lefse-plot_res.py tax-otu-table-result.txt tax-otu-table-diffabund.pdf” properly and got this error:

Traceback (most recent call last):

  • File “/home/gethsimani/miniconda3/envs/lefse/bin/lefse-plot_res.py”, line 177, in *
  • else: plot_histo_hor(params[‘output_file’],params,data,len(data[‘cls’]) == 2,params[‘report_features’])*
  • File “/home/gethsimani/miniconda3/envs/lefse/bin/lefse-plot_res.py”, line 70, in plot_histo_hor*
  • ax = fig.add_subplot(111,frame_on=False,axis_bgcolor=params[‘back_color’])*
  • File “/home/gethsimani/miniconda3/envs/lefse/lib/python2.7/site-packages/matplotlib/figure.py”, line 1257, in add_subplot*
  • a = subplot_class_factory(projection_class)(self, *args, *kwargs)
  • File “/home/gethsimani/miniconda3/envs/lefse/lib/python2.7/site-packages/matplotlib/axes/_subplots.py”, line 77, in init*
  • self._axes_class.init(self, fig, self.figbox, *kwargs)
  • File “/home/gethsimani/miniconda3/envs/lefse/lib/python2.7/site-packages/matplotlib/axes/_base.py”, line 541, in init*
  • self.update(kwargs)*
  • File “/home/gethsimani/miniconda3/envs/lefse/lib/python2.7/site-packages/matplotlib/artist.py”, line 888, in update*
  • for k, v in props.items()]*
  • File “/home/gethsimani/miniconda3/envs/lefse/lib/python2.7/site-packages/matplotlib/artist.py”, line 881, in _update_property*
  • raise AttributeError(‘Unknown property %s’ % k)*
    AttributeError: Unknown property axis_bgcolor

To begin the analysis, I ran the commands reported in the link Lefse after QIIME2, to prepare qiime2 files for LEfSe and then I ran the following commands:

$ lefse-format_input.py collapse.table.txt tax-otu-table-form.txt -c 1 -u 2 -o 1000000
(There is no subclass in my data & I have to admit that I am not sure what -o argument means)

run_lefse.py tax-otu-table-form.txt tax-otu-table-result.txt lefse-plot_res.py tax-otu-table-result.txt tax-otu-table-diffabund.pdf
$ lefse-plot_cladogram.py tax-otu-table-result.txt tax-otu-table-cladogram.pdf

I have read similar topics in the forum, but most of them referred to categorical data (eg groups of normal, overweight, underweight individuals), while as you can see on the file attached (collapse.table.txt), my data include numerical values. The attached file includes metadata concerning a growth factor, the samples_ID and OTU IDs found in qiime2 analysis.

Can LEfSe perform this type of quantitative analysis, or should I try a different tool? Do you have something in mind? Is there something wrong with the format of the file I use as input in LEfSe?

Thank u for your time!

collapse.table.txt (21.3 KB)