Is anyone can suggest which tool can be used to produce the figure below when I have metatranscriptome data and paired metagenome data?
This was something I made using Python’s plotting utilities. It’s not from a special tool/ / HUMAnN utility, though maybe we could add one in the future. 
This is a scatter plot on log axes where the 0s have been replaced by a small value in order to plot them in the x,y margins. The plot also includes a best-fit line to the non-zero points in log space (which is also how we do our mtx ~ mgx modeling, so the line reflects what the model “sees”). I colored the points based on our phenotype of interest to highlight cases where the phenotype was consistently above/below the best-fit line. I.e. cases where the EC was consistently over/under expressed in the phenotype relative to its gene-copy number.
Hope this helps!
Hi Eric,
The tool you made is really cool. Hope it can go to public in tutorial in the future.
-Chao