The bioBakery help forum

Hallagram error cmap?

I am running into an error trying to run hallagram. I am on a Mac osx 10.11.6 & have just installed halla and its dependencies using pip so should be the most up-to-date version of program as of today.

hallagram similarity_table.txt hypotheses_tree.txt associations.txt --outfile hallagram.pdf
usage: hallagram [-h] [–strongest STRONGEST] [–largest LARGEST] [–mask]
[–cmap CMAP] [–axlabels AXLABELS AXLABELS]
[–outfile OUTFILE] [–similarity SIMILARITY]
[–orderby ORDERBY]
simtable tree associations
hallagram: error: unrecognized arguments: hallagram.pdf
(base) cassie-ettingers-macbook-pro:halla_its_16s_output Cassie$ hallagram $hallagram similarity_table.txt hypotheses_tree.txt associations.txt --outfile hallagram.pdf
Traceback (most recent call last):
File “/opt/miniconda3/bin/hallagram”, line 8, in
File “/opt/miniconda3/lib/python3.7/site-packages/halla/”, line 354, in main
File “/opt/miniconda3/lib/python3.7/site-packages/halla/”, line 269, in plot
File “/opt/miniconda3/lib/python3.7/site-packages/matplotlib/”, line 450, in init
cbook._check_isinstance([colors.Colormap, None], cmap=cmap)
File “/opt/miniconda3/lib/python3.7/site-packages/matplotlib/cbook/”, line 2128, in _check_isinstance
TypeError: ‘cmap’ must be an instance of matplotlib.colors.Colormap or None, not a str

Dear all.

I am also encountering the exact same error. I tried to explicitly specify --cmap in the command to one of the colourmap names, but to no avail.

Thank you very much.