Publication Sequence ID Matrices
I have an alignment of protein sequences that I have aligned with MUSCLE using the Bio3D package in R. I have then created a sequence identity matrix and heatmap using seqidentity() and the plot() functions. My question is this - what do you look for in sequence ID matrices in publications? The plan for this matrix is to eventually be put into a publication and therefore I am looking for recommendations regarding this.
Thanks!
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Putting a figure in a publication then asking what should be said about this figure is putting the cart before the horse. A figure should be used as evidence to support an argument made in the paper so ask yourself what it is that you want this figure to say. Depending on the answer, this particular plot may or may not be relevant.