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tyjo / coptr

Accurate and robust inference of microbial growth dynamics from metagenomic sequencing
GNU General Public License v3.0
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Feature Request: Visualization #9

Closed brendanwee closed 3 years ago

brendanwee commented 3 years ago

It would be nice to visualize the coverage maps of the species that had PTR predicted.

I was able to create a simple one by just taking all the read locations and creating a histogram, but I'm guessing that is probably a bit naive.

tyjo commented 3 years ago

The estimate step has a --plot argument that plots binned read counts along the genome and model fit. The argument takes a folder, and outputs one plot for each predicted PTR. Is this similar to your thinking?

The --plot argument was missing from the estimate specification in the documentation. I updated it just now.

brendanwee commented 3 years ago

Yes that is exactly what I was thinking. Thank you!

On Fri, Aug 27, 2021 at 4:11 PM Tyler @.***> wrote:

The estimate step has a --plot argument that plots binned read counts along the genome and model fit for each predicted PTR. Is this similar to your thinking?

The --plot argument was missing from the estimate specification in the documentation. I updated it just now.

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tyjo commented 3 years ago

I'm going to close this issue. Feel free to reopen if you have any other questions.