I am trying to plot cladogram in Galaxy/Hutlab. The cladogram does not show all the species names in the legend which are represented in the image. I would really appreciate some insight into this matter.
It looks like you have many features that are differentially expressed in your dataset. To highlight the strongest associations (and remove visual clutter from the plot) I’d recommend increasing your LDA threshold from the default (2.0) to a higher value (4.0 is a good start).
I hope that helps!