903a638e8959f088ca1c82531eded597c6c305bc
kent
  Fri Jan 22 04:21:18 2021 -0800
Coloring all of fetalGeneAtlas subtracks with same scheme. Coloring hepatocytes.

diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt
index a28e1de..4b9bc09 100644
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@ -34299,37 +34299,37 @@
 
 # Figure out the geneset they used and generate mapping file
 gencodeVersionForGenes gene.lst /hive/data/inside/geneSymVerTx.tsv -bed=mapping.bed
 # best is gencodeV19 as id on hg19 with 60284 of 63562 (94.8428%) hits
 
 
 # Turn some into barChart, and then bigBarChart
 foreach s (cell_type Assay Experiment_batch donor Organ Organ_cell_lineage RT_group sex)
     matrixToBarChartBed clust/$s.matrix mapping.bed clust/$s.bed -stats=bbi/$s.stats -trackDb=clust/$s.ra
     bedSort clust/$s.bed clust/$s.bed
     bedToBigBed clust/$s.bed /hive/data/genomes/hg19/chrom.sizes bbi/$s.bb -type=bed6+3 -as=/cluster/home/kent/src/hg/lib/simpleBarChartBed.as
 end
 
 # Make up special colors for cell_type.  First manually create two column 
 # file that relates at least some of sample labels to cell types we have colors for.
-# Call this file clust/cell_type.labels.  
-matrixClusterColumns clust/cell_type.matrix clust/cell_type.labels cluster clust/cell_type.unnormed clust/cell_type.restats
+# Call this file cell_type.labels.  
+matrixClusterColumns clust/cell_type.matrix cell_type.labels cluster clust/cell_type.unnormed clust/cell_type.restats
 matrixNormalize column sum clust/cell_type.unnormed clust/cell_type.ref
-hcaColorCells clust/cell_type.ref ../typeColors.tsv clust/cell_type.matrix clust/cell_type.refStats -trackDb=clust/cell_type.colors -stats=bbi/cell_type.stats
+#hcaColorCells clust/cell_type.ref ../typeColors.tsv clust/cell_type.matrix clust/cell_type.refStats -trackDb=clust/cell_type.colors -stats=bbi/cell_type.stats
 
 # Use same colors for some others
-foreach s (Experiment_batch donor Organ Organ_cell_lineage RT_group)
+foreach s (cell_type Assay Experiment_batch donor Organ Organ_cell_lineage RT_group sex)
     hcaColorCells clust/cell_type.ref ../typeColors.tsv clust/$s.matrix clust/$s.refStats -trackDb=clust/$s.colors -stats=bbi/$s.stats
 end
 
 # Link files needed by browser at runtime to the /gbdb dir
 mkdir /gbdb/hg19/bbi/fetalGeneAtlas
 foreach s (cell_type Assay Experiment_batch donor Organ Organ_cell_lineage RT_group sex)
     ln -s /hive/data/genomes/hg19/bed/singleCell/fetalGeneAtlas/bbi/$s.bb /gbdb/hg19/bbi/fetalGeneAtlas/
     ln -s /hive/data/genomes/hg19/bed/singleCell/fetalGeneAtlas/bbi/$s.stats /gbdb/hg19/bbi/fetalGeneAtlas/
 end
 
 
 hgBbiDbLink hg19 fetalGeneAtlasCellTypes /gbdb/hg19/bbi/fetalGeneAtlas/cell_type.bb
 hgBbiDbLink hg19 fetalGeneAtlasDonor /gbdb/hg19/bbi/fetalGeneAtlas/donor.bb
 hgBbiDbLink hg19 fetalGeneAtlasAssay /gbdb/hg19/bbi/fetalGeneAtlas/Assay.bb
 hgBbiDbLink hg19 fetalGeneAtlasExperiment /gbdb/hg19/bbi/fetalGeneAtlas/Experiment_batch.bb