Add in circular plotting

[siddC]

Add in a genoVi and plotly function to generate circular plots showcasing phylon gene location per strain.

Main Plotly function

• plot_phylon_locations(phylon_name, gff_file, reference_genome):

• Parameters:

  • eggNOG annotations file (part of NmfData)
  • gff_file (part of NmfData)
  • reference_genome (genome_id or list of genome_id): Reference Genome ID(s)

• Returns: plotly interactive plot (fig) with interactive circular map

Logic:

• 1 function for processing gff files (return list of genes in a strain in order: per strain which is dict key)

• 1 function for finding common genes (100% of strains)

  • Future work: n-1, n-2 thresholding

• 1 function for finding common genes (makes sure it only happens once)

  • Find strains which were filtered out from this function and (future work:) analyze them

• 1 big function that creates strain groups

• 1 function for reference order (used for mapping) and mapping

• 1 big function to make dataframes

• 1 function for plotting

Additional work:

• Make sure it works for chromosomes+plasmids

For NmfData:

• We need to process ALL gff files prior to running (only needs to happen ONCE) [lazy method implementation]
• Have Reference Genome property (make sure it can be set, can also be a list)
  • This may not exist

For downloads.py:

• Can search for reference genomes