docs v2: custom chrom ordering (bigwig)

[manzt]

BigWig Files
""""""""""""

In this example, we'll set up a server containing both a chromosome labels
track and a bigwig track. Furthermore, the bigwig track will be ordered
according to the chromosome info in the specified file.

.. code-block:: python


    from higlass.client import View, Track
    from higlass.tilesets import bigwig, chromsizes
    import higlass.tilesets

    chromsizes_fp = '../data/chromSizes_hg19_reordered.tsv'
    bigwig_fp = '../data/wgEncodeCaltechRnaSeqHuvecR1x75dTh1014IlnaPlusSignalRep2.bigWig'

    with open(chromsizes_fp) as f:
        chromsizes_arr = []
        for line in f.readlines():
            chrom, size = line.split('\t')
            chromsizes_arr.append((chrom, int(size)))

    cs = chromsizes(chromsizes_fp)
    ts = bigwig(bigwig_fp, chromsizes=chromsizes_arr)

    tr0 = Track('top-axis')
    tr1 = Track('horizontal-bar', tileset=ts)
    tr2 = Track('horizontal-chromosome-labels', position='top', tileset=cs)

    view1 = View([tr0, tr1, tr2])
    display, server, viewconf = higlass.display([view1])

    display

The client view will be composed such that three tracks are visible. Two of them
are served from the local server.

.. image:: img/jupyter-bigwig.png

We don't currently support custom chromsizes in the top-level hg.bigwig. Should be easy enough to add, but here is the current boilerplate:

import higlass as hg
from higlass.tileset import LocalTileset
from clodius.tiles.bigwig import tiles, tileset_info

chromsizes = [...]
fp = '../data/wgEncodeCaltechRnaSeqHuvecR1x75dTh1014IlnaPlusSignalRep2.bigWig'

ts = hg.server.add(
    LocalTileset(
        tiles=functools.partial(tiles, fp, chromsizes=chromsizes),
        info=functools.partial(tileset_info, fp, chromsizes=chromsizes),
        uid="demo",
    ),
)

hg.view(
    ts.track('chromosome-labels'),
    ts.track('horizontal-bar'),
)