feature requests

[yhoogstrate]

Dear @brj0 ,

very very cool package, thanks for making it available under a MIT License.

• Would it be possible to include the option in the CLI to run a single sample
• Would it be possible to make the export the CNV plot as a png/svg ?

Especially the latter would be really helpful to quickly check through our patient samples what's going on

all best,

Youri

[brj0]

Hi Youri,

At the moment, we are focusing on preparing a publication, so we are not adding new features right now. In the future, we may expand the CLI to support more options, such as running analyses on specific samples.

Regarding exporting CNV plots as PNG or SVG: mepylome only saves the necessary data, so generating these formats directly would be superfluous. Converting plotly plots from HTML to PNG is actually quite slow and can negatively impact performance. For a clinical setup where you need all your patient data local in a directory, I recommend creating a small script to generate the desired outputs locally. You can take inspiration from the script that is very similar to the one we use at our institution.

All best,
Jon