Hi, I have been trying to create a circos image with multiple overlapping tiles that can be visible as overlapping with transparent fill colors. For some reason the transparency of fill color for 2D-data tracks doesn’t seem to work. Is there a work around or is the transparency feature limited to only ideogram bands?
Is this the function?
2D Data Plot → Plot Format Specific Options → Stroke Color Transparency
And, do you mean that adjusting the transparency is not adjusting the resulting graph for that data?
That could be based on the data. Meaning, the data value that the color shading differences are based on, are not different enough to show up differently. (this is hard to explain!). You could try testing with fake data values, or maybe that is what you have done already?
If you want to share a simple example, we can ask the developer who wrote this wrapper for advice. Actually, let’s just cc them now and see what they think. cc @hexylena
for example I am making two tiles that over lap each other (one of them has greater thickness and different inside radius from the other). In 2D Data Plot → tiles → Plot Format Specific Options → Fill color transparency, I chose a low value for transparency. However, I can’t see the transparency effect. I have played around with Z-index and different colors.
It works with histograms but not with tiles.
Thanks for explaining. I don’t think Circos itself was designed to handle overlapping tiles in a way that isn’t “stacked”. So, that may be part of the problem. Ref: http://circos.ca/tutorials/lessons/2d_tracks/tiles/
Is the transparency handled correctly if your two tiles are modified to not overlap? (just as a test)