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CCDM-Programming-Club / codonfriend

Analyse Codon Usage With Your Pals
MIT License
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Chromo plot CAI #8

Open paulamool opened 6 years ago

paulamool commented 6 years ago

Feature will plot the gene CAI chromosome locations

  1. read in genome FASTA, GFF3 and CAI information
  2. Build a data frame of GFF3 positions and CAI information
  3. Color code the CAI
  4. Plot gene locations to genome for visualization

Will look at linear and circular plots of genomes

darcyabjones commented 6 years ago

This is great!

Can we break this up into smaller parts so we can divvy it up a bit? Maybe the table and the plotting should be separate?

What would you use the fasta for? Could that input also be a ".genome" file?

paulamool commented 6 years ago

Sure, let's split it up by step?. Yes we don't need the genome FASTA, couldn't edit my comment

darcyabjones commented 6 years ago

Hi Paula,

I've split the steps up into slightly more atomic issues that can be tackled separately. See #11 #10 #9

I thought this issue would still work for the discussion plotting the data.

I think for circular plots, circlize is a good option. For flat plots, ggplot2 still works, but there's also ggbio and a few other dedicated options for plotting genomic data.