Cladogram plotting issue (error?)

Downstream analysis and statistics LEfSe
1

I’m running a conda install of lefse1.0.8.

/anaconda3/envs/lefse1.0.8/share/lefse-1.0.8.post1-2

The cladograms it generates have the shading misaligned. They seem to be aligning so that they are not centered on the clade but instead shade clockwise, starting at the center of the clade. This has been consistent across multiple datasets. In the figure attached, the shading should be rotated about 60 degrees counter-clockwise, ie the large green region should be centered on the p_Bacteroidetes clade at the top.

Any clues how to fix this?

Thanks,

CLD
CLD1200×968 198 KB

2

The same data processed through the Huttenhower Galaxy server plots fine.

CLD_galaxy
CLD_galaxy800×547 90.9 KB

3

bump. please. bump. thanks.

4

Hi Doyle,

Thanks for pointing out this issue! We have seen similar plotting problem with the background annotation. We are working on the fix to this issue. In the meantime as you have shown you can either use the galaxy forum or we have found that installing GraPhlAn in its own conda environment will also fix this issue until we can push the fix to the main tool.

Best,
Kelsey