Plotting extracted clusters using plot_clusters
¶
By default, the visualisation offered by cblaster
shows only a heatmap of query hits
per result cluster. While this is very useful for quickly identifying patterns in large
datasets, we generally still want to see how these clusters compare in a more
biologically relevant way.
The plot_clusters
module allows you to do precisely this. Given a session and some
filters to choose specific clusters (exactly like in the extract_clusters
module),
this module will automatically extract the clusters, then generate an interactive
visualisation showing each cluster to-scale using clinker
(doi: 10.1093/bioinformatics/btab007,
https://github.com/gamcil/clinker).
Example usage¶
Minimum working example:
$ cblaster plot_clusters session.json
Plot clusters 1-10 and cluster 25 (these numbers can be found in the summary file of the ‘search’ command):
$ cblaster plot_clusters session.json -c 1-10 25 -o plot.html
Plot only from specific organisms (regular expressions):
$ cblaster plot_clusters session.json -or "Aspergillus.*" "Penicillium.*" -o plot.html
Plot only clusters from a specific range on scaffold_123 and all clusters on scaffold_234 (note: assumes unique scaffold names):
$ cblaster plot_clusters session.json -sc scaffold_123:1-80000 scaffold_234 -o plot.html