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/mm10/singleCellSignalsPeaks.txt src/hg/makeDb/doc/mm10/singleCellSignalsPeaks.txt index 69a7ad01e47..3594e984eb9 100644 --- src/hg/makeDb/doc/mm10/singleCellSignalsPeaks.txt +++ src/hg/makeDb/doc/mm10/singleCellSignalsPeaks.txt @@ -34,30 +34,40 @@ # 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) ############################################################################## # copySingleCellSignalsPeaksFiles.py copies every cellBrowserMm10 subtrack file # into /hive/data/genomes/mm10/bed/singleCellSignalsPeaks/<served-relpath>, # keeping each file's served relative path, and copies the composite's facet # metadata to <bed>/singleCellSignalsPeaks_metadata.tsv. The served subpath is # preserved on purpose: some coverage/peak basenames (e.g. MOL.bw, OPC.bw) repeat # across datasets, so a flat directory would clobber them. 89.6 GB, 647 files. # +# The same script also writes <bed>/singleCellSignalsPeaks_colors.json, the track's +# colorSettingsUrl target: {"Cell_class": {<class>: "#RRGGBB"}}, rendered straight from +# celltype-palette.tsv. The faceted UI draws a color swatch beside each checkbox of any +# facet named in that file, so the Cell class checkboxes carry the same colors the +# subtracks are drawn in. Keys must match the metadata column value verbatim -- the +# lookup in facetedComposite.js is an exact string match, and an unmatched key just +# leaves that swatch blank. The whole palette is written for both assemblies, so classes +# an assembly does not use (mm10 uses all 23; hg38 has no Ependymal or Choroid plexus) +# are simply unused keys. +# # scriptDir=$HOME/kent/src/hg/makeDb/scripts/singleCellSignalsPeaks # python3 $scriptDir/copySingleCellSignalsPeaksFiles.py --assembly mm10 --dry-run # python3 $scriptDir/copySingleCellSignalsPeaksFiles.py --assembly mm10 ############################################################################## # 3. Generate the trackDb .ra ############################################################################## # makeSingleCellSignalsPeaksRa.py reads the hub's mm10 stanzas, keeps the # cellBrowserMm10 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). # The generator also: drops any subtrack whose source path is under a deprecated # "*.old/" dir, sets every subtrack "off" by default (users pick tracks from the # faceted selector), and assigns "priority" by cell class so same-class tracks # group together in the display. Labels/colors/facets are already resolved by @@ -75,31 +85,32 @@ # doc/hg38/singleCellSignalsPeaks.txt). # # Cell type: the source cluster label is cleaned and, for datasets with coded # cluster names, mapped to a canonical name via a paper-curated crosswalk # (celltype-crosswalks/<collection>.tsv; codes decoded from Li 2021 PMID 34616068, # Zhang 2022 PMID 36207411, Zhu 2021 PMID 33589836, and the Allen whole-brain # taxonomy). Redundant synonyms are merged, QC clusters (doublet / low-quality / # batch) are dropped, and commas become ';' (the faceted UI tokenizes cell # values on commas). The full cell type is a searchable table column (_Cell_type), # not a facet -- there are too many values. # # Cell class: each cell type is assigned one of 23 broad classes # (celltype-crosswalks/celltype-class.tsv, built by build_celltype_crosswalks.py). # The class drives BOTH the track color (one colorblind-conscious palette, # celltype-palette.tsv, shared by hg38 and mm10 so a class is the same color on -# both assemblies) and the subtrack priority. Cell class is the primary cell facet. +# both assemblies) and the subtrack priority. Cell class is the primary cell facet, +# and the same palette is published as the facet swatch colors (section 2). # # "Other glia" (88,160,88) was added because "Other" was doing four unrelated # jobs. Of 40 tracks corpus-wide sitting in it: 14 real glia with nowhere else to # go, 14 peripheral glia deliberately placed there (Schwann / enteric -- left # alone), 5 that are not cell types at all (All cell types / All cells / # Neuronal and glial -- aggregate peak calls, a separate defect NOT addressed), # and 6 genuinely other. The new class takes the glial aggregate labels (Glia, # Glial), olfactory ensheathing cells, and the five fly glia subtypes; Schwann and # enteric glia stay under "Other". Named for symmetry with the existing # "Other neuron". The color came from a grid search maximizing minimum dE against # the 22 existing entries under normal, deuteranope and protanope simulation, # restricted to the widest free hue band; nearest neighbours are Epithelial # (dE 17) and Astrocyte (dE 20), both above the palette's own closest pair # (Other vs Unknown, 12.7). Before this, Glia and Non-Neuronal were both grey. #