I was able to run through the LEfSe process until the last step for plotting.
The data used for my analysis is attached. Lefsetest.txt (166.0 KB)
Thank you so much for your help!!
Here is the error message:
Traceback (most recent call last):
File “/shed_tools/testtoolshed.g2.bx.psu.edu/repos/george-weingart/lefse/a6284ef17bf3/lefse/./plot_res.py”, line 151, in
else: plot_histo_hor(params[‘output_file’],params,data,len(data[‘cls’]) == 2)
The problem is caused by there being spaces in your Treatment labels. I was able to plot the features by changing the labels from, for example, “0% RPS” to “0%RPS” (see attachment).
I hope that helps!
Lefsetest_edit.txt (166.0 KB)
Many thanks for the help!!!
Now I have a new question.
How do I enforce the treatment order numerically sequential such as 0 %, 2%, 5%, 10%?
Right nor it is 0%, 10%, 2%, 5%.
Thanks a lot.
Unfortunately, there is no way I know of to order the labels other than alphanumerically. Since “1” comes before “2”, it reads “10” as coming before “2”. The only way I know to order the groups how you want is to name them a_0% b_2% c_5% d_10% or something similar.
Thanks a lot for your answers, Meg.
I ran into a new problem today.
With the same exact format as other datasets that produced perfect legends. The new dataset (attached) does not have legend. What could be the problem?
Many thanks again.
Celinepred_metagenome_Test.txt (502.3 KB)
Unfortunately, I’m not able to reproduce the problem–I was able to plot this with a legend (see below). Is this similar to what your figure looks like, except for the legend?