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molbio-dresden / flexidot

Highly customizable, ambiguity-aware dotplots for visual sequence analyses
GNU Lesser General Public License v2.1
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Self plot shading #8

Open jiadong324 opened 5 years ago

jiadong324 commented 5 years ago

Dear author,

I go through SupplementaryData.pdf and found the example of using .gff3 to annotate the plot. But how can I add the figure legend, I did not see the legend on my data either your test data.

Thanks!

molbio-dresden commented 5 years ago

Dear @jiadong324,

thank you for contacting us and detailing your question. We generate extra files containing the legends. The GFF shading legend will have a similar name as your dotplot, including the string "Shading_Legend". Can you check and tell us, if this file has been generated?

In the legend file two alternative legends are provided for the user to choose (horizontal and vertical orientation).

Best wishes!

jiadong324 commented 5 years ago

@molbio-dresden

Thanks for your feedbacks. I found the legend in another file, but I suggest to have the legend in the dotplot figure.

molbio-dresden commented 5 years ago

Dear @jiadong324,

Good that you found the file. Thank you for the suggestion to include the legend in the dotplot file, which is certainly more intuitive.

Actually, the "legend issue" has been a matter of debate among the authors. In our early FlexiDot versions we even had this implemented. We noticed that automatic legend positioning often obscures or transforms part of the dotplot, and thus leads to less clear pictures. At least for our dotplot use, we found that we prefer to have the legend separate and settled for this flexible solution in the public versions. We cannot really say it this point, but we will keep your suggestion in mind and discuss about making this optional at some point.

Best wishes from Dresden.