Question about preprocessing and considerations for generating a heatmap from FastANI --matrix output #153
Description
Hello,
I am working on system development for the Department of Biology at Chung-Ang University in Korea.
We are planning to generate a heatmap in R using the FastANI --matrix output, and we would like to ask whether there are any recommended preprocessing steps, implementation considerations, or caveats we should be aware of.
In particular, we would appreciate your guidance on the following:
1. Is the --matrix output the recommended input for generating a heatmap in R?
2. Are there any recommended preprocessing steps before using this output for heatmap visualization?
3. Is it appropriate to convert the lower triangular matrix into a full symmetric matrix before plotting?
4. How should missing genome-pair comparisons or low-ANI pairs be handled during matrix conversion and visualization?
5. If there is any recommended script, workflow, or best practice for this post-processing step, we would greatly appreciate your advice.
Our goal is to implement the heatmap generation logic appropriately and interpret the visualization results correctly.
Thank you very much for your time and help.