This is my first Bokeh server app.
Here is what it does:
- loads up a fasta file with coding sequences (DNA) and a whole genome (DNA)
- calculates the z-score-normalized codon distribution in all coding sequences
- applies PCA to the dataframe with the codon distributions
- plots a scatter plot of the PCA data
- serves the codon distribution of a single selected data point in form of a bar diagram
- calculates the melting temperature of chunks of the genome and plots a ring plot, colored accordingly.
If you make a copy of the environment
in which I worked on this app, you can run bokeh serve genome_codon_usage_app.py --show in the directory to which you cloned the app.
That should give you something like the screenshot below in which I used the zoom tool to zoom in a little bit and marked a single point.
