nf-core
Make `circos` plots optional in the `orange` report
If there are many structural driver events identified by Purple, the Orange report might be very long and big in file size due to the circos plots displayed for each of the reportable drivers individually, which may be in the order of hundreds. To prevent this, the user might want to skip or limit the circos plots in the final report. I suggest to make this part to be optional based on a config parameter in the Linx config so that the user may choose this optionally. Alternatively, a tool parameter to plot a maximum of n number of plots can be specified after ranking the driver events. Currently, I get like hundreds of circos plots in the Orange report which is dozens of pages long and several hundreds of MB file size which makes the report hard to navigate and share.
Hi @bounlu, this is an issue that I've run into myself and have thought about ways to solve, including an approach similar to your suggestion. For the oncoanalyser 1.0.0 release there wasn't a straightforward solution since the particular version of ORANGE used always required LINX plot inputs.
The latest release of ORANGE no longer has this requirement for LINX plot inputs, so this can be addressed in the next oncoanalyser release. I would say the most simple approach would to be avoid including LINX plots in the ORANGE report if there are more than some user-configurable amount.
I'll add this to our milestones for the 2.0.0 release, thanks!
This will be reviewed after the upcoming release, de-scoping from that release accordingly