The bioBakery help forum

Manipulate plots


I have 2 questions regarding plotting.

  1. If there are more levels in the class, the plot looks like it just recycles colors.
  2. How can I manipulate the legends for the class/samples, they are overlapping with the main plot.


Hi there,

To really manipulate the cladogram from LEfSe we suggest pulling out the final data and using GraPhlAn to plot your data (which is what LEfSe is already using). Within GraPhlAn you can set your own colors and many other factors within the cladogram.


I hope this helps!

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