550a0e2666bcce27181a0cb0eab32ed261e444f6 mspeir Thu Aug 27 14:56:42 2026 -0700 singleCellSignalsPeaks: color the Cell class facet checkboxes, refs #37820, refs #37914 The faceted UI already draws a color swatch beside each checkbox of any facet named in a colorSettingsUrl JSON, and the track already colors its subtracks by broad cell class from celltype-palette.tsv. Publish that palette so the selector shows the same colors: copySingleCellSignalsPeaksFiles.py now writes <bed>/singleCellSignalsPeaks_colors.json alongside the facet metadata, and the composite header names it. Rendered from the one shared palette, so a class is the same color in the checkbox list, in the drawn tracks, and on both assemblies. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> diff --git src/hg/makeDb/doc/hg38/singleCellSignalsPeaks.txt src/hg/makeDb/doc/hg38/singleCellSignalsPeaks.txt index 34dac1a5c5f..ca007866604 100644 --- src/hg/makeDb/doc/hg38/singleCellSignalsPeaks.txt +++ src/hg/makeDb/doc/hg38/singleCellSignalsPeaks.txt @@ -1,133 +1,140 @@ # hg38 singleCellSignalsPeaks track - 2026-07-20 Claude (mspeir) refs #37820 # The native hg38 "singleCellSignalsPeaks" faceted composite is the Genome # Browser version of the UCSC Cell Browser all-tracks super hub (Redmine #37820). # The hub build lives in the cellBrowser repo, ucsc/allTracksHub: # https://github.com/ucscGenomeBrowser/cellBrowser/tree/develop/ucsc/allTracksHub # # It gathers the per-cell-type signal (bigWig) and peak (bigBed / bigNarrowPeak) # tracks from the single-cell ATAC datasets in the Cell Browser and re-parents # them under one faceted composite. cCREs and interactions live in their own # composites in the hub and are NOT part of this track. ############################################################################## # 1. Source data ############################################################################## # The track mirrors the hub's main hg38 signal-&-peaks faceted composite # (cellBrowserHg38). That composite and its facet metadata are produced by the # hub build from the Cell Browser dataset tree (/hive/data/inside/cells/datasets): # # cd $HOME/cellBrowser/ucsc/allTracksHub # python3 build_manifest.py # scan datasets -> manifest.tsv # python3 build_stanzas.py # manifest -> stanzas/hg38.trackDb.txt # # + meta/hg38.metadata.tsv # # The build writes its output to $CBHUB_OUT, NOT next to the scripts (that dir is # git-controlled). Default: /hive/data/inside/cells/all-tracks-hub-build # # The per-track source files (abs_path column of manifest.tsv) are the files the # Cell Browser datasets already serve; nothing is regenerated here, only copied. ############################################################################## # 2. Copy the data files into place (bed dir, served via a /gbdb symlink) ############################################################################## # Every subtrack of the cellBrowserHg38 composite is copied into # /hive/data/genomes/hg38/bed/singleCellSignalsPeaks/<served-relpath> # keeping each file's served relative path (e.g. # human-enhancer-atlas/.../Adipocyte.bw , # allen-brain-science/seaad_MTG/bw/ADNC0Astro.bw ). # The served subpath is preserved on purpose: 18 peak-file basenames repeat # across datasets (cortex-atac), so a flat directory would clobber them. # 934 files total (bigWig + bigBed/bigNarrowPeak), ~274 GB as the copy script # counts it (256 GiB; du reports 511 G because of GPFS block allocation). # # copySingleCellSignalsPeaksFiles.py skips files already up to date (same size and # a destination no older than its source), so a re-run after new data lands moves # only the new files -- adding the 9 stage-split brainvar bigWigs took ~1.2 GB and # 10 seconds even though the summary line still counts all 934 subtracks. # # 11 data files in the bed dir are no longer referenced by the .ra (134 MB): the 10 # cortex-atac interact.old/ bigBeds reclassified to the interact composite and one # dropped QC cluster. Harmless, and both are explained above; delete them if the # dir is ever tidied. # # The file list comes straight from the composite's bigDataUrl lines mapped back # to manifest abs_paths; copy each abs_path to bed/<relpath> (mkdir -p parents). ############################################################################## # 3. Generate the trackDb .ra ############################################################################## # makeSingleCellSignalsPeaksRa.py reads the hub's hg38 stanzas, keeps the # cellBrowserHg38 subtracks, renames the composite to singleCellSignalsPeaks, # repoints every bigDataUrl at the local /gbdb copy, and writes the .ra with # group=regulation (ATAC signal/peaks sit with the ENCODE regulatory tracks). # Subtrack colors and labels carry through from the hub stanzas. # # Colors are the shared broad-cell-class palette, NOT each dataset's own scheme -- # SEA-AD used to come through in its own subclass colors, and no longer does, so a # cell class is one color across every dataset and both assemblies. See # doc/mm10/singleCellSignalsPeaks.txt sections 4 and 4b. # # scriptDir=$HOME/kent/src/hg/makeDb/scripts/singleCellSignalsPeaks # python3 $scriptDir/makeSingleCellSignalsPeaksRa.py \ # --stanzas $CBHUB_OUT/stanzas/hg38.trackDb.txt \ # --out $HOME/kent/src/hg/makeDb/trackDb/human/hg38/singleCellSignalsPeaks.ra # # https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/singleCellSignalsPeaks ############################################################################## -# 4. Facet metadata +# 4. Facet metadata and facet colors ############################################################################## # The faceted composite's metaDataUrl points at a copy of the hub's hg38 # main-faceted metadata (primaryKey = Track): # # cp $CBHUB_OUT/meta/hg38.metadata.tsv \ # /hive/data/genomes/hg38/bed/singleCellSignalsPeaks/singleCellSignalsPeaks_metadata.tsv +# +# Its colorSettingsUrl points at singleCellSignalsPeaks_colors.json in the same dir, +# which gives the faceted UI a color swatch for each Cell class checkbox, matching the +# color the subtracks of that class are drawn in. Both files are written by +# copySingleCellSignalsPeaksFiles.py (section 2); the JSON is rendered from the shared +# celltype-palette.tsv, so it is identical on hg38 and mm10. See +# doc/mm10/singleCellSignalsPeaks.txt section 2 for the format and its gotchas. ############################################################################## # 5. Labels, colors, and facets ############################################################################## # The cell type / cell class / shortLabel / longLabel / color / facet values are # all derived by build_stanzas.py, not copied from the source hubs. That logic # (paper-curated cell-type crosswalks, the shared broad-class color palette, the # rebuilt short and long labels, the variant descriptors that keep every label # unique, and the per-collection tissue/life-stage/condition parsing incl. SEA-AD # region + ADNC) is documented once in doc/mm10/singleCellSignalsPeaks.txt # section 4; it runs identically for hg38. Tracks are colored by broad cell class # from the same palette as mm10, so a class is the same color on both assemblies. # # hg38-specific label notes: # - cortex-atac calls peaks three ways and serves all three for each cell type. # The method is a filename suffix on some files (AstroOligo_MACSpeaks.bb) and # the containing directory on others (MACSpeaks/AstroOligo.bb) -- both layouts # appear in the same dataset and the two files are genuinely different peak # sets, so both forms are detected and named in the label. # - human-enhancer-atlas rolls tissue-qualified fibroblast/endothelial clusters # (Fibro_Muscle, Endothelial_General_2) up to one cell type; the source code # goes in the label so the clusters stay distinguishable. # - SEA-AD shortLabels carry a compact region + ADNC token (Astrocyte MTG A0), # since the longLabel distinction alone would leave eight identical short # labels per cell type (2 regions x 4 ADNC levels). ############################################################################## # Counts ############################################################################## # 934 subtracks across 9 datasets: human-enhancer-atlas (444), # sea-ad-brain-atac (184), cortex-atac (81), retina (69), neuro-degen-atac (66), # multiomic-human-heart (40), cardiogenesis-atac (19), olg-eae-ms (18), # brainvar (13). Mislabeled interaction bigBeds (cortex-atac interact.old/) are # reclassified to the interact composite and QC clusters are dropped before the # .ra is written. Facet metadata rows match the subtracks 1:1. # All 934 longLabels are unique; shortLabels are <=22 chars with no underscores. # Every subtrack has a broad cell class and a palette color (0 unclassified). # One track legitimately shows class "Unknown": neuro-degen-atac's cluster whose # source label is literally "Unannotated". That is a real palette class, not a # classification failure. # # brainvar went 4 -> 13 subtracks when the group sent stage-split pseudobulk # coverage: 5 prenatal and 4 postnatal added alongside the 4 original # combined-stage tracks. Progenitors are prenatal only, so 9 new files, not 10. # Their methods text says "a tile size of 1 kb" but the data is 100 bp (every # interval is 100 bp wide on 100 bp boundaries, matching the TileSize-100 # filenames); 100 bp is what the description page states. Worth confirming with # them which they intended.