a3fd570e96fb63b45d583ebcce83d8d23673a30a max Wed Sep 16 07:00:11 2026 -0700 hg38 pcLAI: squish, not dense - dense removes the details page Same problem the GenArk contrib collection had: in tvDense hgTracks draws one merged row per subtrack and emits no per-item map boxes, so there is no hgc link and no mouseOver, and the ancestry scatterplot built for the details page is unreachable. On chr18:10,800,000-12,500,000 the image map has 0 hgc links in dense and 134 in squish. The composite is now visibility squish plus onlyVisibility squish. On a composite that governs the only vis dropdown the track has, since the subtracks get checkboxes rather than dropdowns, and hgTrackUi now offers Hide and Squish. Squish suits the data: the windows tile without overlapping and carry no item labels, so each haplotype stays one row at a 20 Mb view, refs #35415 diff --git src/hg/makeDb/scripts/hprcPclai/hprcPclaiMakeTrackDb.py src/hg/makeDb/scripts/hprcPclai/hprcPclaiMakeTrackDb.py index 15c2f8dde0f..cdff2037ef4 100755 --- src/hg/makeDb/scripts/hprcPclai/hprcPclaiMakeTrackDb.py +++ src/hg/makeDb/scripts/hprcPclai/hprcPclaiMakeTrackDb.py @@ -1,130 +1,136 @@ #!/usr/bin/env python3 """Write the trackDb stanzas for the hg38 hprcPclai composite track. One subtrack per HPRC Release 2 haplotype, read from the pcLAI GRCh38-coordinate index CSV, so the track follows whatever the index lists rather than a hardcoded sample list. Subtracks are grouped by sample and haplotype so hgTrackUi draws a sample-by-haplotype matrix instead of a flat list of several hundred checkboxes. detailsScript and metaDataUrl are repeated on every subtrack rather than set once on the composite. Both are read as local settings at the point they are used: bigBedClick.c collects detailsScript.* with trackDbLocalSettingsWildMatch(), and hgTrackUi's file fetch looks the path up on the tdb of the clicked track, so a value on the parent alone would not be seen. hprcPclaiMakeTrackDb.py defaultOnFile holds one "." per line, the subtracks that start out checked; blank lines and # comments are ignored. """ import sys import csv TRACK = "hprcPclai" GBDB = "/gbdb/$D/hprcPclai" DATA_VERSION = "HPRC Release 2, pcLAI v1.1 (GRCh38 coordinates)" # Only four coordinates ever appear in the centroid field across all haplotypes: # the four ancestry clusters pcLAI discretizes to. They would make a good # categorical filter, but each value contains a comma and comma is the separator # filterValues uses, so filtering on them needs a comma-free label field first. DETAILS_SCRIPT = ('{"dataUrl":"pclaiRefPanel.json","exportFields":["pca","centroid"],' '"title":"Position in ancestry space","xLabel":"PC1","yLabel":"PC2"}') def readIndex(fname): """Return [(sample, haplotype)] from the HPRC index CSV, sorted by sample.""" rows = [] with open(fname, encoding="utf-8", newline="") as fh: for row in csv.DictReader(fh): samp = (row["sample_id"] or "").strip() hap = (row["haplotype"] or "").strip() if samp and hap: rows.append((samp, hap)) if not rows: sys.exit("no rows in %s" % fname) return sorted(set(rows)) def readDefaultOn(fname): on = set() with open(fname, encoding="utf-8") as fh: for line in fh: line = line.split("#")[0].strip() if line: on.add(line) return on def main(): if len(sys.argv) != 4: sys.exit(__doc__) idxFname, onFname, outFname = sys.argv[1:4] haps = readIndex(idxFname) wanted = readDefaultOn(onFname) samples = sorted({s for s, _h in haps}) hapVals = sorted({h for _s, h in haps}) out = open(outFname, "w", encoding="utf-8") w = out.write w("# hg38 pcLAI local ancestry, one subtrack per HPRC Release 2 haplotype.\n") w("# Generated by hg/makeDb/scripts/hprcPclai/hprcPclaiMakeTrackDb.py -- do not\n") w("# hand-edit; see hg/makeDb/doc/hg38/hprcPclai.txt.\n\n") w("track %s\n" % TRACK) w("compositeTrack on\n") w("shortLabel pcLAI Ancestry\n") w("longLabel Point cloud local ancestry inference (pcLAI) along HPRC assembly haplotypes\n") w("group hprc\n") w("type bigBed 9 +\n") w("itemRgb on\n") - w("visibility dense\n") + # squish, not dense, and pinned there. In tvDense hgTracks draws one merged row + # per subtrack and emits no per-item map boxes at all, so the scatterplot on the + # details page and the mouseOver below both become unreachable. squish keeps + # every map box, and since the windows tile without overlapping each haplotype + # still collapses to one or two thin rows instead of pack's ~50. + w("visibility squish\n") + w("onlyVisibility squish\n") w("priority 30\n") # A whole chromosome holds a few thousand windows per haplotype, well over the # 1000-item default at which pack mode gives up drawing; the block structure # this track exists to show is only visible at that zoom. w("maxItems 40000\n") w("subGroup1 sample Sample %s\n" % " ".join("%s=%s" % (s, s) for s in samples)) w("subGroup2 hap Haplotype %s\n" % " ".join("h%s=%s" % (h, h) for h in hapVals)) w("sortOrder sample=+ hap=+\n") w("dimensions dimensionY=sample dimensionX=hap\n") w("dragAndDrop subTracks\n") w("dataVersion %s\n" % DATA_VERSION) w("\n") # Explicit priorities: without them the subtracks come out in an arbitrary # (in practice reversed) order in the image, and with several hundred rows a # stable sample order is what makes the display readable. nOn = 0 for prio, (samp, hap) in enumerate(haps, start=1): key = "%s.%s" % (samp, hap) sub = "%s%sH%s" % (TRACK, samp.replace("-", ""), hap) on = key in wanted nOn += on w(" track %s\n" % sub) w(" parent %s %s\n" % (TRACK, "on" if on else "off")) w(" subGroups sample=%s hap=h%s\n" % (samp, hap)) w(" priority %d\n" % prio) w(" shortLabel %s\n" % key) w(" longLabel pcLAI ancestry of HPRC assembly %s haplotype %s\n" % (samp, hap)) w(" type bigBed 9 +\n") w(" bigDataUrl %s/%s.bb\n" % (GBDB, key)) w(" itemRgb on\n") w(" mouseOver ${haplotype} ${window}
Window PC1,PC2: ${pca}" "
Ancestry centroid: ${centroid}
Confidence: ${score}\n") w(" detailsScript.scatterPlot.pca %s\n" % DETAILS_SCRIPT) w(" metaDataUrl %s/pclaiRefPanel.json\n" % GBDB) w("\n") out.close() missing = wanted - {"%s.%s" % (s, h) for s, h in haps} if missing: sys.stderr.write("WARNING: default-on not in index: %s\n" % ", ".join(sorted(missing))) sys.stderr.write("%s: %d subtracks, %d samples, %d on by default\n" % (outFname, len(haps), len(samples), nOn)) if __name__ == "__main__": main()