When evaluating tandem repeat regions in dotplots, it is useful to look at the ratio of the width-to-height of the tandem repeat rectangle. Proper interpretation of such rectangles requires that the basepair:pixel aspect ratio be the same for both axes. Could you make the aspect ratios match for the two axes, at least for the REF v REF and ALT v ALT plots?
Here is an example (DEL00121927SUR from the HG002 GIAB evaluation set) where the REF v REF plot has a non-square tandem repeat region along its main diagonal.
When evaluating tandem repeat regions in dotplots, it is useful to look at the ratio of the width-to-height of the tandem repeat rectangle. Proper interpretation of such rectangles requires that the basepair:pixel aspect ratio be the same for both axes. Could you make the aspect ratios match for the two axes, at least for the REF v REF and ALT v ALT plots?
Here is an example (DEL00121927SUR from the HG002 GIAB evaluation set) where the REF v REF plot has a non-square tandem repeat region along its main diagonal.