Hi Cameron,
First of all, thank you for clinker — it's an excellent tool that has become a staple in our comparative genomics workflow.
I'd like to request a feature that would greatly improve the utility of clinker for publication figures: the ability to toggle gene labels on a per-track basis, rather than globally for all sequences.
Use case: When comparing multiple strains against a single reference sequence, it is standard practice in publications to display gene labels only on the reference (top) track, keeping the strain tracks below clean and uncluttered. Currently, clinker either shows labels on all tracks or none, which makes it difficult to generate publication-ready figures without post-processing in Inkscape or similar tools.
Proposed implementation: A simple toggle in the clustermap.js sidebar allowing the user to show/hide labels per sequence track individually, similar to how other visualization tools handle this. Alternatively, a command-line flag such as --label_tracks accepting sequence names or indices would also be very useful.
This would save users significant time in post-processing and make clinker even more suitable for direct publication use.
Thank you for considering this request.
Best regards,
Konstantinos Valourdos
M.Sc. Bioinformatics and Computational Biology, NKUA
Hi Cameron,
First of all, thank you for clinker — it's an excellent tool that has become a staple in our comparative genomics workflow.
I'd like to request a feature that would greatly improve the utility of clinker for publication figures: the ability to toggle gene labels on a per-track basis, rather than globally for all sequences.
Use case: When comparing multiple strains against a single reference sequence, it is standard practice in publications to display gene labels only on the reference (top) track, keeping the strain tracks below clean and uncluttered. Currently, clinker either shows labels on all tracks or none, which makes it difficult to generate publication-ready figures without post-processing in Inkscape or similar tools.
Proposed implementation: A simple toggle in the clustermap.js sidebar allowing the user to show/hide labels per sequence track individually, similar to how other visualization tools handle this. Alternatively, a command-line flag such as --label_tracks accepting sequence names or indices would also be very useful.
This would save users significant time in post-processing and make clinker even more suitable for direct publication use.
Thank you for considering this request.
Best regards,
Konstantinos Valourdos
M.Sc. Bioinformatics and Computational Biology, NKUA