No taxa labels after lefse_plot_cladogram.py

Downstream analysis and statistics LEfSe
1

Hi,

I couldnt get any taxa labels after generating cladogram via lefse_plot_cladogram.py within conda environment. I also check all the usage options, however still no taxa labels at right side.

cladogramL6
cladogramL61920×2033 205 KB

There is also no access to Galaxy module. Therefore, I couldnt find a solution to get a progress. Since I need to complete the analysis within few days, I would be grateful for any help!! Thank you

2

Hi,

I have the same problem, and also tried all the usage options.

image
image560×560 101 KB

Until now, the Galaxy module is still no access. [503 Service Unavailable]

I would be grateful for any help!
Thank you.

Kenken

3

Hi,

I can see taxa level by opening resulting .svg files by Adobe Illustrator.
The legend seems to be shown outside the canvas.

4

I am currently facing the same issue. Have you found any solution?

5 
plt.savefig(out_file,format=params['format'],facecolor=params['back_color'],edgecolor=params['fore_color'],dpi=params['dpi'], bbox_inches='tight')

https://github.com/SegataLab/lefse/blob/1.1.2/lefse/lefse_plot_cladogram.py#L338

I found that the problem should be bbox_inches=‘tight’, delete it and taxa can be displayed

plt.savefig(out_file,format=params['format'],facecolor=params['back_color'],edgecolor=params['fore_color'],dpi=params['dpi'])