Metaphlan 2 heat map

Microbial community profiling MetaPhlAn
1

I’m getting the following error when trying to generate a heat map:

higleyadmin@JOAN9000 ~ % metaphlan_hclust_heatmap.py -c bbcry --top 25 --minv 0.1 -s log --in water_metaphlan_combined.txt --out abundance_heatmap.png
Traceback (most recent call last):
File “/opt/anaconda/envs/python2/bin/metaphlan_hclust_heatmap.py”, line 481, in
tax_lev = pars[‘tax_lev’]
File “/opt/anaconda/envs/python2/bin/metaphlan_hclust_heatmap.py”, line 452, in hclust
heatmap_panel( fig, D, minv, maxv, idx1, idx2, cm_name, scale, sample_labels, feat_labels, label_font_size, -cm_h8.0/ysize, cm_h0.88.0/ysize, flabelon, slabelon, cm_ticks, gridon, ydend_offset+sdend_h8.0
/ysize )
File “/opt/anaconda/envs/python2/bin/metaphlan_hclust_heatmap.py”, line 235, in heatmap_panel
axisbg=bottom_col)
File “/opt/anaconda/envs/python2/lib/python2.7/site-packages/matplotlib/figure.py”, line 1149, in add_axes
a = projection_class(self, rect, **kwargs)
File “/opt/anaconda/envs/python2/lib/python2.7/site-packages/matplotlib/axes/_base.py”, line 541, in init
self.update(kwargs)
File “/opt/anaconda/envs/python2/lib/python2.7/site-packages/matplotlib/artist.py”, line 888, in update
for k, v in props.items()]
File “/opt/anaconda/envs/python2/lib/python2.7/site-packages/matplotlib/artist.py”, line 881, in _update_property
raise AttributeError(‘Unknown property %s’ % k)
AttributeError: Unknown property axisbg
higleyadmin@JOAN9000 ~ %

Any ideas?

2

Hi, which version of matplotlib have you installed?

3

I checked my conda install and it has matplotlib 2.2.3

4

The metaphlan_hclust_heatmap.py script is deprecated, I’d advise you for using hclust2 for heatmap visualization. The script is removed in MetaPhlAn 3.0.

If you have a conda environment for MetaPhlAn3, you can clone the hclust2 repo and use from it, it has all the right dependencies installed.

5

Thank you. The new script works fine. There should be a mention of the deprecation in the documentation.