I am running the LEfSe module locally. I am attempting to process and plot my data, but I’m not getting a legend when I plot the cladogram. I suspect this may be due to the class/group names being incorrectly processed. I
The top of my data file looks like this:
Group | 1 | 2 | 1 | 2 | 1 | 2 | 2 | 1 | 2 | 1 | 2 | 2 | 1 | 1 | 1 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
name | JYL_7_1_2_L001_R1_001 | JYL_6_1_1_L001_R1_001 | JYL_10_1_5_L001_R1_001 | JYL_5_2_0_L001_R1_001 | JYL_9_3_4_L001_R1_001 | JYL_9_1_3_L001_R1_001 | JYL_10_4_6_L001_R1_001 | JYL_15_1_8_L001_R1_001 | JYL_13_1_7_L001_R1_001 | JYL_26_1_11_L001_R1_001 | JYL_26_3_12_L001_R1_001 | JYL_18_1_9_L001_R1_001 | JYL_28_1_13_L001_R1_001 | JYL_33_1_14_L001_R1_001 | JYL_24_1_10_L001_R1_001 |
Bacteria | Actinobacteria | 33219 | 20022 | 8300 | 2237 | 9476 | 16156 | 15016 | 1148 | 11127 | 2168 | 2417 | 2870 | 18122 | 8260 |
Bacteria | Bacteroidetes | 2724 | 8166 | 2475 | 16820 | 6528 | 3423 | 10939 | 14979 | 8868 | 2932 | 30961 | 4377 | 673 | 1700 |
I have processed my data using lefse_format_input.py with these flags “-c 1 -u 2 -o 1000000” and then executed lefse_run.py to create the .res file.
Here is the top of the resulting .res file:
Bacteria.Actinobacteria | 4.310612689030659 | - | ||
---|---|---|---|---|
Bacteria.Bacteroidetes | 4.363902188063198 | - | ||
Bacteria.Chlamydiae | 0.23186646960619614 | - | ||
Bacteria.Cyanobacteria | 1.1029480902342559 | - | ||
Bacteria.Deferribacteres | 0.6616523706543642 | - |
I noticed that each line ends with a “-” rather than a group label, but I’m not sure if that’s what’s causing the issue with the missing legend.
Any advice?