Scale "below" plot in GenomeDiagram? about biopython HOT 4 OPEN

I don't understand what you are asking for, and this sort of open question might be better suited to the mailing list.

@widdowquinn - Any comment Leighton?

from biopython.

Oh, I am sorry, I didn't know about the mailing list, otherwise I would've started asking all these questions there.

I looked a bit at the code and found a parameter "centre", which, as I thought, could help to move the x-axis to zero-level or even any other level. But I understood, why nothing is said about it in the documentation - it influences the y-axis scale. The specified value actually becomes the centre of y-axis... But maybe it is possible to easily adjust the code, so it would work? The code is quiet complicated (or I don't know Python that well), so it is difficult for me to understand it.

It seems, that the drawing order is defined in GenomeDiagram/_LinearDrawer in lines 302-304 and GenomeDiagram/_CircularDrawer in lines 295-298: order of elements in these lists corresponds with there future order of drawing. BTW, I think this list should be present in the documentation, as it is a useful knowledge. And I think there should be a mechanism to adjust the drawing order when creating diagrams.

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In terms of 'layers' - the tracks hold 'sets' (FeatureSet or GraphSet objects), which are rendered in the Z-order they are provided, and within a GraphSet, graphs are rendered in the order they are added to the GraphSet (I think this is stated in the original documentation: http://biopython.org/DIST/docs/GenomeDiagram/userguide.pdf) so it is possible to structure your image to take advantage of this. You can adjust the order when constructing your figure - by providing graphs/sets in the order you want - back to front (just like in Powerpoint/Illustrator, etc. - unlike those packages, this is intended to be programmatic, not interactive rendering).

You can also put the scale line on a separate track by itself, with its own height, so it's not such an obvious gap, if you want the horizontal scale not to overlay on the data. You can then choose to place this track 'below' the track that contains the data.

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So you suggest one should create an "extra" track with no data, but with scale, and for all other track to have no scale. And then place that scaling track the first one to all the levels, and then add all others?

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