Commits for kent

v409_base to v410_preview (2021-01-18 to 2021-01-25) v410

e2d27ce7b87c27ded55ea090a72364bd0327d75b Thu Jan 14 11:49:59 2021 -0800

• Adding lungTravaglini2020 dataset with both 10x and FACS arms.
  • src/hg/makeDb/trackDb/human/hg38/lungTravaglini2020.ra - lines changed 314, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 1, context: html, text, full: html, text

04540fddd609dd1ff407d4907c89d8fa9e178f38 Thu Jan 14 11:53:20 2021 -0800

• Adding -cellMin option to improve coloring of FACS based data sets.
  • src/hca/hcaColorCells/hcaColorCells.c - lines changed 6, context: html, text, full: html, text

59e2aee12d89650eba71c72ffebc62f26c74dc22 Thu Jan 14 15:59:20 2021 -0800

• Adding descriptions of how fetalGeneAtlas and skinSoleBoldo single cell RNA barchart supertracks were made.
  • src/hg/makeDb/doc/hg19.txt - lines changed 161, context: html, text, full: html, text

51a9b5ae84b3979930d70a05b0fcf82a178e2678 Thu Jan 14 19:30:51 2021 -0800

• Adding skinSoleBoldo and liverMacParland single cell data sets.
  • src/hg/makeDb/trackDb/human/hg38/liverMacParland.ra - lines changed 79, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/skinSoleBoldo.ra - lines changed 76, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 2, context: html, text, full: html, text

8a5f4201a85c4d12a6efe6a7c6955a4e6e53de61 Fri Jan 15 08:47:15 2021 -0800

• Making checking on label counts matching matrix dimensions more robust, and catching file close error.
  • src/utils/matrixRelabel/matrixRelabel.c - lines changed 26, context: html, text, full: html, text
  • src/utils/matrixRelabel/test.col - lines changed 1, context: html, text, full: html, text
  • src/utils/matrixRelabel/test.long - lines changed 11, context: html, text, full: html, text
  • src/utils/matrixRelabel/test.row - lines changed 1, context: html, text, full: html, text
  • src/utils/matrixRelabel/test.short - lines changed 2, context: html, text, full: html, text

1174aa23ca05f247d28cec79b7bb2b86ff90811b Fri Jan 15 09:36:35 2021 -0800

• Adding pancreasBaron single cell RNA track to hg38
  • src/hg/makeDb/trackDb/human/hg38/pancreasBaron.ra - lines changed 67, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 1, context: html, text, full: html, text

859a32a5037bf85d25806b4d9a21e0c78ca1289a Fri Jan 15 10:57:32 2021 -0800

• Adding colonWang, ileumWang, and rectumWang single cell RNA datasets.
  • src/hg/makeDb/trackDb/human/hg38/colonWang.ra - lines changed 41, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/ileumWang.ra - lines changed 41, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/rectumWang.ra - lines changed 41, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 3, context: html, text, full: html, text

3e71ea091b2f5ca3c882f8fc09909aaff75c64d4 Fri Jan 15 11:38:44 2021 -0800

• Stretching bars a little by reducing barChartLimit for Wang intestinal data sets.
  • src/hg/makeDb/trackDb/human/hg38/colonWang.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/ileumWang.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/rectumWang.ra - lines changed 1, context: html, text, full: html, text

4a264baa33ac4a9116494b4369309178fd2727b3 Fri Jan 15 13:57:08 2021 -0800

• skinSoleBoldo single cell rna to hg19
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 1, context: html, text, full: html, text

68fb75be28315352c3047092ecdd85c9b5e62086 Fri Jan 15 13:58:05 2021 -0800

• Finished labels on bloodHao single cell RNA on hg38
  • src/hg/makeDb/trackDb/human/hg38/bloodHao.ra - lines changed 60, context: html, text, full: html, text

ddc40a5ed80272c0156240193c65cd1b1d6ee61a Fri Jan 15 13:59:05 2021 -0800

• Making cortexVelmeshev data set on hg38 a little less loud.
  • src/hg/makeDb/trackDb/human/hg38/cortexVelmeshev.ra - lines changed 1, context: html, text, full: html, text

db744228f428826b9eb757d8536fe21da6250b19 Fri Jan 15 14:00:18 2021 -0800

• reducing volume on a bars in heart and lung single cell data sets.
  • src/hg/makeDb/trackDb/human/hg38/heartCellAtlas.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/lungTravaglini2020.ra - lines changed 1, context: html, text, full: html, text

00feb5dea48777b397362387c307086d7268f3fa Sat Jan 16 10:11:49 2021 -0800

• Adding placentaVentoTorma single cell RNA seq data set.
  • src/hg/makeDb/trackDb/human/hg38/placentaVentoTormo.ra - lines changed 189, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 1, context: html, text, full: html, text

5bdcedbdb55631ea78fe3896542e21d6e314c21f Sat Jan 16 10:18:32 2021 -0800

• Adjusting view limits of ss2 subset. It seems to be scaled about the same as the 10x somehow, or close to it, so bringing it back to the same, unlike in the lungTrav. dataset.
  • src/hg/makeDb/trackDb/human/hg38/placentaVentoTormo.ra - lines changed 4, context: html, text, full: html, text

85e43277a71fa053c5e71502e4307738e7971e98 Sat Jan 16 10:42:21 2021 -0800

• Adding this data file since it is important and not under source code control elsewhere, and is used by hcaColorCells at runtime most of the time.
  • src/hca/hcaColorCells/typeColors.tsv - lines changed 30, context: html, text, full: html, text

2f718ddd0797fc5c618bac72c546008d596ca9c1 Sun Jan 17 09:42:52 2021 -0800

• Making scaling of barChart bar widths overall slightly wider, and allowing more modulation.
  • src/hg/hgTracks/barChartTrack.c - lines changed 13, context: html, text, full: html, text

3cacf62418cf270f09b8b10df1daae429f191522 Sun Jan 17 11:39:41 2021 -0800

• Catching error condition of meta row labels not matching up to matrix column labels.
  • src/utils/matrixClusterColumns/matrixClusterColumns.c - lines changed 26, context: html, text, full: html, text

c9066a2a9f398731accc46749ee4e986ec79b6c2 Sun Jan 17 16:15:55 2021 -0800

• Slightly improved coloring scheme for cells, mostly sorted by color.
  • src/hca/hcaColorCells/typeColors.tsv - lines changed 30, context: html, text, full: html, text

57dac7ba30fa3754d63f0046abf01a42b127f1ec Sun Jan 17 18:40:03 2021 -0800

• Commenting out lungVieiraBraga.ra until have time to curate their columns down to 20 for the great merged display.
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 1, context: html, text, full: html, text

272888a64de727315e0328a74b727d695fcb8db7 Mon Jan 18 20:26:56 2021 -0800

• Some fine adjustments to the scale of bars - honestly could make them wider but not wanting to make GTEX behave differently just yet.
  • src/hg/hgTracks/barChartTrack.c - lines changed 7, context: html, text, full: html, text

22ee4e58588dbf633ee93b9c661e08349ff8e908 Mon Jan 18 20:28:29 2021 -0800

• Fixing it so underbar and space should be equivalent in the bar chart labels in the stats file.
  • src/hg/hgc/barChartClick.c - lines changed 14, context: html, text, full: html, text

6eaed8d72f6b12600d7fc8f6bb94b14e396b0948 Mon Jan 18 20:31:32 2021 -0800

• Adding in refGene name2 column search as basically the last thing to try. The way it selects the best transcript out of the refGene pile-up is pretty ad-hoc, just favoring protein coding and better curated, and often just taking the first of many equivalently scoring ones.
  • src/hg/utils/gencodeGeneSymVerTx/gencodeGeneSymVerTx.c - lines changed 182, context: html, text, full: html, text

bf1922c6259ffc74a2041b8e8beb681fe5c927ff Mon Jan 18 20:33:04 2021 -0800

• Adding -miss and -target options. -target will look harder for hits within a database. -miss puts unmapped genes into a miss file.
  • src/hg/utils/gencodeVersionForGenes/gencodeVersionForGenes.c - lines changed 100, context: html, text, full: html, text

13f8af77f35302e6f64b8d3c34eeb40f23a2588f Mon Jan 18 20:35:46 2021 -0800

• Recoloring and in some cases merging columns.
  • src/hg/makeDb/trackDb/human/hg38/colonWang.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/cortexVelmeshev.ra - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/fetalGeneAtlas.ra - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/heartCellAtlas.ra - lines changed 23, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/ileumWang.ra - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/kidneyStewart.ra - lines changed 35, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/liverMacParland.ra - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/lungTravaglini2020.ra - lines changed 77, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/muscleDeMicheli.ra - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/pancreasBaron.ra - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/placentaVentoTormo.ra - lines changed 43, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/rectumWang.ra - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/skinSoleBoldo.ra - lines changed 8, context: html, text, full: html, text

73c045c8fce9058a333220a2f72e5750d5cd885a Mon Jan 18 20:37:32 2021 -0800

• Recoloring.
  • src/hg/makeDb/trackDb/human/hg19/fetalGeneAtlas.ra - lines changed 19, context: html, text, full: html, text

6d4fc5c83c417afe88dc436f03117f0c128dfda9 Tue Jan 19 09:40:18 2021 -0800

• Updating mapping.bed and statistics
  • src/hg/makeDb/doc/hg19.txt - lines changed 3, context: html, text, full: html, text

3d815b5ddda4f027ed21ddc71995eebec2a8574b Wed Jan 20 01:46:40 2021 -0800

• This utility to help merge expression matrices across data sets built on different gene models is starting to work.
  • src/hca/hcaUnifyMatrix/hcaUnifyMatrix.c - lines changed 402, context: html, text, full: html, text
  • src/hca/hcaUnifyMatrix/makefile - lines changed 4, context: html, text, full: html, text

bfd7d15166c13c243f9d9a4bf1d6d50f168c4920 Wed Jan 20 09:14:39 2021 -0800

• Adding trackDb and stats options. Also adding scale factor per dataset.
  • src/hca/hcaUnifyMatrix/hcaUnifyMatrix.c - lines changed 85, context: html, text, full: html, text

43ebc9fee33b23d8ac12a77441a5e2140c0bcb0b Wed Jan 20 09:15:44 2021 -0800

• Adjusting padding and barWidth when have lots of bars.
  • src/hg/hgTracks/barChartTrack.c - lines changed 7, context: html, text, full: html, text

280f594f5ec2f99725f2d7b5effa38827d8a3694 Wed Jan 20 09:17:27 2021 -0800

• Adding singleCellMerged track.
  • src/hg/makeDb/trackDb/human/hg38/singleCellMerged.ra - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 1, context: html, text, full: html, text

7fd0b76aeb83144a908f8c15e6a5452ded39bed1 Wed Jan 20 09:19:41 2021 -0800

• Fixing bug where was ommitting thickEnd from bed output.
  • src/hg/utils/gencodeVersionForGenes/gencodeVersionForGenes.c - lines changed 2, context: html, text, full: html, text

8e7dfd6577aea4f69a73b8f6ff6885cc1d05088b Thu Jan 21 09:33:11 2021 -0800

• Oops, forgot to include this.
  • src/hg/makeDb/trackDb/human/hg19/skinSoleBoldo.ra - lines changed 78, context: html, text, full: html, text

58ecdffac6432e41d3a1a8d355e0e2eeda6e6d5d Thu Jan 21 13:41:35 2021 -0800

• Tweaking bar widths and spacing at different scales.
  • src/hg/hgTracks/barChartTrack.c - lines changed 18, context: html, text, full: html, text

24302c51b7a95f59436da8eb263b10706bc0ab9a Fri Jan 22 04:14:24 2021 -0800

• Reducing verbosity of status output.
  • src/hca/hcaUnifyMatrix/hcaUnifyMatrix.c - lines changed 4, context: html, text, full: html, text

6a6d27d0f45a9cb2a4f783f4641f0b2a0ecdca69 Fri Jan 22 04:16:19 2021 -0800

• Making right label of how big bar is use same calculations for string width as the left labels, and in process preventing them from getting clipped as often.
  • src/hg/hgc/barChartClick.c - lines changed 14, context: html, text, full: html, text

903a638e8959f088ca1c82531eded597c6c305bc Fri Jan 22 04:21:18 2021 -0800

• Coloring all of fetalGeneAtlas subtracks with same scheme. Coloring hepatocytes.
  • src/hg/makeDb/doc/hg19.txt - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/fetalGeneAtlas.ra - lines changed 35, context: html, text, full: html, text

a60ebb6be3010ad11c415ca1fabc3f5bdec86c09 Fri Jan 22 04:23:39 2021 -0800

• Shifting to common colors shared by others, sadly a little less distinct for this data set. Shifting from L2 to L1, less detailed, cell type annotations for main cell_type.
  • src/hg/makeDb/trackDb/human/hg38/bloodHao.ra - lines changed 31, context: html, text, full: html, text

7c4a3360752f7a5c32f2abb96d0af76036fb5043 Fri Jan 22 04:26:14 2021 -0800

• Lumping some cells, mostly immune, with small counts into an 'other' category in the pancreas. Making 'detailed cell type' track for unlumped version.
  • src/hg/makeDb/trackDb/human/hg38/pancreasBaron.ra - lines changed 26, context: html, text, full: html, text

52a806f70c35f8bdb1b7db3217203c591695c0ac Fri Jan 22 04:28:43 2021 -0800

• Changing scale from 0-2 to 0-100 for best viewing and calling units 'vn-100.' Reintegrating things to take in changes in component tracks, especially reducing number of categories in blood by a lot and pancreas by a little.
  • src/hg/makeDb/trackDb/human/hg38/singleCellMerged.ra - lines changed 4, context: html, text, full: html, text

44cb9d5b6cdf1e4182e727d4f858da45fcc04bff Fri Jan 22 10:42:00 2021 -0800

• Updating colors and fixing 'sorted by' to be 'binned by' like elsewhere
  • src/hg/makeDb/trackDb/human/hg19/fetalGeneAtlas.ra - lines changed 40, context: html, text, full: html, text