anvi-display-codon-frequencies
Table of Contents
Display codon frequency statistics across genes in a given genome in the anvi'o interactive interface..
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Authors
Can consume
contigs-db 
profile-db collection 
bin 
Can provide
Usage
This program interactively displays gene-level codon frequency patterns across a set of contigs.
The program calculates gene-level frequencies of individual codons and displays them in a matrix format where each row represents a codon (ordered by the amino acids they encode), each column represents a single gene, and the data points represent the counts (or frequency, depending on user-provided parameters) of occurrence of a given codon in a given gene. By default, the program orders each gene based on their synteny (the conserved order of genes across genomes) to reveal patterns in codon usage throughout the genome.
This program is most effectively applied to a contigs-db that represents a single genome. Its utility for revealing synteny-based patterns of codon usage increases with decreasing numbers of contigs (i.e., a complete genome with a single contig will provide much better visualization than a metagenome-assembled genome (MAG) with 200 contigs, even though the program will visualize the latter adequately).
The calculation of different frequency statistics depends on a range of options, and the tool relies upon the same library that anvi-get-codon-frequencies uses.
Default output
The simplest form of this command is the following:
anvi-display-codon-frequencies -c contigs-db
When run this way, the program will generate a blank profile-db as a temporary file and will display the counts of each codon across each gene in the genome.
Here is an example with GCF_001458775.1, a reference genome for Nitrospira nitrificans:
anvi-display-codon-frequencies -c GCF_001458775.db
Which will display the following:
Here, every data point represents the actual count of a given codon in a given gene. As a result, very long genes that produce very large counts for each codon lead to the suppression of all other counts. It is possible to use any of the interactive interface capabilities to improve the visualization of data (such as setting up min/max values for layer data points, etc). It is also possible to run the program with additional parameters.
Additional parameters
Additional parameters available through the help menu of the program will help filter genes and functions, as well as determine how the data are normalized. For instance, the following command will exclude genes that are shorter than 100 nucleotides long, exclude the stop codon as well as those codons for amino acids methionine, tryptophan, and cysteine, normalize data within synonymous codons (codons that encode the same amino acid), and replace all empty values in output with 0.0:
anvi-display-codon-frequencies --gene-min-codons 100 \
--exclude-amino-acids STP Met Trp Cys \
--synonymous \
--infinity-to-zero \
-c GCF_001458775.db
Which will display the following:
Please see the help menu for a complete list of parameters.
Visualization features
Once the display is shown, the genes can also be ordered based on hierarchical clustering of the codon frequencies using the Settings panel, and then selecting the ‘Codon frequencies’ option from the ‘Order’ menu and clicking Draw to bring together those genes that show similar codon usage patterns regardless of their location in the genome:
Bin selection is possible in all visualizations, and clicking on the button that shows the number of genes in a given bin in the Bins panel will open a window that displays their functions:
Working with a profile-db
By default, the program will initiate a blank profile-db, a temporary file stored under a directory that will be cleaned up by the operating system regularly. This means that storing states and bins, and re-running anvi-display-codon-frequencies will not bring the stored data back.
Alternatively, the user can define a specific location for a profile-db, upon which the program would generate a blank profile at this precise location:
anvi-display-codon-frequencies -c GCF_001458775.db \
-p GCF_001458775-PROFILE.db
This profile-db can be used to visualize the same data repeatedly; however, future visualizations will require anvi-interactive rather than anvi-display-codon-frequencies:
anvi-interactive -p GCF_001458775-PROFILE.db \
--manual
Edit this file to update this information.
Additional Resources
Are you aware of resources that may help users better understand the utility of this program? Please feel free to edit this file on GitHub. If you are not sure how to do that, find the __resources__ tag in this file to see an example.