Commits for kate

v324_preview2 to v324_base (2015-10-19 to 2015-10-26) v324

• Some initial display work for GTEX gene expression track. refs #13504
  
  • src/hg/hgTracks/hgTracks.h - lines changed 3, context: html, text, full: html, text
  • src/hg/hgTracks/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/hgTracks/simpleTracks.c - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 6, context: html, text, full: html, text
• Merge branch 'master' into gtex
  
• Fix options syntax
  
  • src/hg/makeDb/outside/hgGtexGeneBed/hgGtexGeneBed.c - lines changed 2, context: html, text, full: html, text
• GTEX track display: Add hgc to show tissue color table. Add debug statements for hgTracks. Also doc. This is version demoed at SAB. refs #13504
  
  • src/hg/hgTracks/hgTracks.c - lines changed 10, context: html, text, full: html, text
  • src/hg/hgc/hgc.c - lines changed 75, context: html, text, full: html, text
  • src/hg/hgc/hgc.h - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/gtex/2014-jan.txt - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg19.txt - lines changed 37, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 2, context: html, text, full: html, text
• Download recent eQTL data. refs #13504
  
  • src/hg/makeDb/doc/gtex/2014-jan.txt - lines changed 9, context: html, text, full: html, text
• Conflict resolution
  
  • src/hg/hgTracks/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/hgc/hgc.c - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg19.txt - lines changed 122, context: html, text, full: html, text
• First cut GTEX gene track display. refs #13504
  
  • src/hg/hgTracks/gtexTracks.c - lines changed 177, context: html, text, full: html, text
• Merge branch 'master' into gtex
  
• Correct sample and tissue counts in track label. refs #13504
  
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 2, context: html, text, full: html, text
• Add alternate displays for different zoom levels. refs #13504
  
  • src/hg/hgTracks/gtexTracks.c - lines changed 58, context: html, text, full: html, text
• Merge branch 'master' into gtex
  
• Minor work on GTEX details during meeting (much more needed). refs #13504
  
  • src/hg/hgc/hgc.c - lines changed 18, context: html, text, full: html, text
• Merge branch 'master' into gtex
  
  • src/hg/hgc/hgc.c - lines changed 87, context: html, text, full: html, text
• Get new GTEX data and the color scheme, from GTEX portal. Follow-up from 2015 GTEX meeting. refs #13504
  
  • src/hg/inc/gtexTissue.h - lines changed 5, context: html, text, full: html, text
  • src/hg/lib/gtexTissue.as - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/gtexTissue.c - lines changed 24, context: html, text, full: html, text
  • src/hg/lib/gtexTissue.sql - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/gtex/2014-jan.txt - lines changed 3, context: html, text, full: html, text
• Merge branch 'master' into gtex
  
• Add support for GTEX tissue color scheme. refs #15645
  
  • src/hg/hgTrackUi/hgTrackUi.c - lines changed 4, context: html, text, full: html, text
  • src/hg/hgTracks/gtexTracks.c - lines changed 51, context: html, text, full: html, text
  • src/hg/inc/gtexTissue.h - lines changed 15, context: html, text, full: html, text
  • src/hg/inc/gtexUi.h - lines changed 19, context: html, text, full: html, text
  • src/hg/inc/hui.h - lines changed 3, context: html, text, full: html, text
  • src/hg/lib/gtexTissue.c - lines changed 36, context: html, text, full: html, text
  • src/inc/memgfx.h - lines changed 5, context: html, text, full: html, text
  • src/inc/rainbow.h - lines changed 3, context: html, text, full: html, text
  • src/lib/rainbow.c - lines changed 16, context: html, text, full: html, text
• Mouseover display of tissues now works a bit better. Still fragile & messy (don't bother reviewing this commit). refs #15645
  
  • src/hg/lib/hui.c - lines changed 20, context: html, text, full: html, text
  • src/hg/makeDb/doc/gtex/2014-jan.txt - lines changed 9, context: html, text, full: html, text
• Mouseover improvements. refs #15645
  
  • src/hg/hgTracks/gtexTracks.c - lines changed 91, context: html, text, full: html, text
• Merge branch 'master' into gtex
  
  • src/inc/memgfx.h - lines changed 4, context: html, text, full: html, text
• Label fix. Clarify imageV2 warning. refs #15645
  
  • src/hg/hgTracks/imageV2.c - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/gtexGeneExpr.html - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 1, context: html, text, full: html, text
• Add squished gene model under expression graph (address concern of SAB and others re anchoring to genome. refs #15645
  
  • src/hg/hgTracks/gtexTracks.c - lines changed 116, context: html, text, full: html, text
• Loaded gene models from GTEX portal. refs #15645
  
  • src/hg/makeDb/doc/gtex/2014-jan.txt - lines changed 21, context: html, text, full: html, text
• Better placement of map boxes for mouseover. refs #15645
  
  • src/hg/hgTracks/gtexTracks.c - lines changed 41, context: html, text, full: html, text
• Add faint gray line under graph to show extent when bars are missing. refs #15645
  
  • src/hg/hgTracks/gtexTracks.c - lines changed 33, context: html, text, full: html, text
• 1. Fix pack problem. 2. Fix map box in dense/squish. refs #15645
  
  • src/hg/hgTracks/gtexTracks.c - lines changed 33, context: html, text, full: html, text
• Minor cleanup
  
  • src/hg/hgTracks/hgTracks.c - lines changed 3, context: html, text, full: html, text
• Add support for comparison graphs (2 graphs, one top and one below inverted, based on splitting samples by sex or age). First cut of display only. refs #15645
  
  • src/hg/hgTracks/gtexTracks.c - lines changed 129, context: html, text, full: html, text
  • src/hg/inc/gtexUi.h - lines changed 15, context: html, text, full: html, text
  • src/hg/lib/hui.c - lines changed 34, context: html, text, full: html, text
• Scale wrt all genes, not just those in window. We now save the max tissue median score in the gtexInfo table. refs #15645
  
  • src/hg/hgTracks/gtexTracks.c - lines changed 43, context: html, text, full: html, text
  • src/hg/inc/gtexInfo.h - lines changed 71, context: html, text, full: html, text
  • src/hg/lib/gtexInfo.as - lines changed 7, context: html, text, full: html, text
  • src/hg/lib/gtexInfo.c - lines changed 162, context: html, text, full: html, text
  • src/hg/lib/gtexInfo.sql - lines changed 13, context: html, text, full: html, text
  • src/hg/lib/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/gtex/2014-jan.txt - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/outside/hgGtex/hgGtex.c - lines changed 37, context: html, text, full: html, text
• Restore a bit of lost code.
  
  • src/hg/inc/gtexTissue.h - lines changed 3, context: html, text, full: html, text
  • src/hg/lib/gtexTissue.c - lines changed 18, context: html, text, full: html, text
• Allow comparison graphs when zoomed out (suppress only when this requires querying the sample db which would be too slow). refs #15645
  
  • src/hg/hgTracks/gtexTracks.c - lines changed 2, context: html, text, full: html, text
• 1. Fix tissue ordering problem (hgGtex). 2. Add stats table (rename gtexTissueData to gtexTissueMedian and use gtexTissueData for stats. 3. Extend gtexInfo table.refs #15645
  
  • src/hg/hgTracks/gtexTracks.c - lines changed 51, context: html, text, full: html, text
  • src/hg/inc/gtexInfo.h - lines changed 23, context: html, text, full: html, text
  • src/hg/inc/gtexTissueData.h - lines changed 30, context: html, text, full: html, text
  • src/hg/inc/gtexTissueMedian.h - lines changed 64, context: html, text, full: html, text
  • src/hg/lib/gtexInfo.as - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/gtexInfo.c - lines changed 49, context: html, text, full: html, text
  • src/hg/lib/gtexInfo.sql - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/gtexSampleData.sql - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/gtexTissueData.as - lines changed 7, context: html, text, full: html, text
  • src/hg/lib/gtexTissueData.c - lines changed 102, context: html, text, full: html, text
  • src/hg/lib/gtexTissueData.sql - lines changed 9, context: html, text, full: html, text
  • src/hg/lib/gtexTissueMedian.as - lines changed 7, context: html, text, full: html, text
  • src/hg/lib/gtexTissueMedian.c - lines changed 158, context: html, text, full: html, text
  • src/hg/lib/gtexTissueMedian.sql - lines changed 13, context: html, text, full: html, text
  • src/hg/lib/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/gtex/2014-jan.txt - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg19.txt - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/outside/hgGtex/hgGtex.c - lines changed 80, context: html, text, full: html, text
  • src/hg/makeDb/outside/hgGtexGeneBed/hgGtexGeneBed.c - lines changed 9, context: html, text, full: html, text
• Create build tool and build tracks of GTEX exon expression. refs #15648
  
  • src/hg/makeDb/doc/gtex/2014-jan.txt - lines changed 52, context: html, text, full: html, text
  • src/hg/makeDb/outside/hgGtexExonBed/hgGtexExonBed.c - lines changed 199, context: html, text, full: html, text
  • src/hg/makeDb/outside/hgGtexExonBed/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/outside/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.gtex.ra - lines changed 495, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 16, context: html, text, full: html, text
• Fix a few bugs - connection handling, bin field in genePred, more color handling - introduced while messing with schemas (to extend features and improve perf). refs #15645
  
  • src/hg/hgTracks/gtexTracks.c - lines changed 40, context: html, text, full: html, text
  • src/hg/inc/gtexTissue.h - lines changed 7, context: html, text, full: html, text
  • src/hg/lib/gtexInfo.c - lines changed 3, context: html, text, full: html, text
  • src/hg/lib/gtexTissue.c - lines changed 19, context: html, text, full: html, text
• Create build tool and build tracks of GTEX exon expression. refs #15648
  
  • src/hg/makeDb/outside/hgGtex/hgGtex.c - lines changed 68, context: html, text, full: html, text
• Schemas for GTEX exon and gene tracks. Likely interim. refs #15648
  
  • src/hg/lib/bed6FloatVal.as - lines changed 12, context: html, text, full: html, text
  • src/hg/lib/bed6FloatVal.sql - lines changed 20, context: html, text, full: html, text
  • src/hg/lib/gtexGeneBed.sql - lines changed 21, context: html, text, full: html, text
• Fix chrM entries in exon files. refs #15648
  
  • src/hg/makeDb/doc/gtex/2014-jan.txt - lines changed 50, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg19.txt - lines changed 48, context: html, text, full: html, text
• Major reorg of track load/draw, prep for computing medians (for filtering and comparison graphs. refs #15645
  
  • src/hg/hgTracks/gtexTracks.c - lines changed 181, context: html, text, full: html, text
• More prep moved to loader. Fix mapping problem in squish mode. refs #15645
  
  • src/hg/hgTracks/gtexTracks.c - lines changed 36, context: html, text, full: html, text
• Implement medians computed on sub-samples (initially for M/F comparison. refs #15645
  
  • src/hg/hgTracks/gtexTracks.c - lines changed 106, context: html, text, full: html, text
• Tweak labels. refs #15645
  
  • src/hg/makeDb/trackDb/human/trackDb.gtex.ra - lines changed 54, context: html, text, full: html, text
• Add labels (e.g. M/F) to comparison graphs. refs #15645
  
  • src/hg/hgTracks/gtexTracks.c - lines changed 74, context: html, text, full: html, text
• Resolving conflict
  
  • src/hg/makeDb/doc/gtex/2014-jan.txt - lines changed 49, context: html, text, full: html, text
• Correct donor count. Just use donors in sample table. refs #13504
  
  • src/hg/makeDb/trackDb/human/trackDb.gtex.ra - lines changed 2, context: html, text, full: html, text
• Expand GTEx sample table. Now includes all fields except RNA-seqC metrics, which if we decide to include them, will likley be in an auxiliary table. refs #13504
  
  • src/hg/inc/gtexSample.h - lines changed 17, context: html, text, full: html, text
  • src/hg/lib/gtexSample.as - lines changed 11, context: html, text, full: html, text
  • src/hg/lib/gtexSample.c - lines changed 77, context: html, text, full: html, text
  • src/hg/lib/gtexSample.sql - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/doc/gtex/2014-jan.txt - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/outside/hgGtex/hgGtex.c - lines changed 60, context: html, text, full: html, text
• Ifdef'ed in Galt's support for multi-region display, so continuing development can consider it. refs #15645
  
  • src/hg/hgTracks/gtexTracks.c - lines changed 190, context: html, text, full: html, text
• Verbosify a debug statement.
  
  • src/lib/common.c - lines changed 1, context: html, text, full: html, text
• 1. Add eQTL and variants tracks. 2. Modify loader to exclude expression table rows with zero-valued scores (shrinks table by half). 3. Prep a data frame for R (make a few plots to explore the data). refs #1350
  
  • src/hg/makeDb/doc/gtex/2014-jan.txt - lines changed 61, context: html, text, full: html, text
  • src/hg/makeDb/outside/hgGtex/hgGtex.c - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.gtex.ra - lines changed 16, context: html, text, full: html, text
• Merge branch 'master' into gtex
  
• Add log transform option to display config. refs #15645
  
  • src/hg/hgTracks/gtexTracks.c - lines changed 29, context: html, text, full: html, text
  • src/hg/inc/gtexUi.h - lines changed 4, context: html, text, full: html, text
  • src/hg/lib/hui.c - lines changed 10, context: html, text, full: html, text
• Reload tissue median table to fix ordering problem in exp list. refs #15645
  
  • src/hg/makeDb/doc/gtex/2014-jan.txt - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg19.txt - lines changed 1, context: html, text, full: html, text
• Move GTEx track details into separate file. refs #13504
  
  • src/hg/hgc/gtexClick.c - lines changed 88, context: html, text, full: html, text
  • src/hg/hgc/hgc.c - lines changed 77, context: html, text, full: html, text
  • src/hg/hgc/makefile - lines changed 1, context: html, text, full: html, text
• First cut gene expression boxplot image for GTEx details page. refs #15645
  
  • src/hg/hgc/gtexClick.c - lines changed 229, context: html, text, full: html, text
• 1. Graph aesthetics (colors, etc.). 2. Change ordering to median descending. refs #15645
  
  • src/hg/hgc/gtexClick.c - lines changed 24, context: html, text, full: html, text
• A stab at adding axes and title to graph for GTEx details page. refs #15645
  
  • src/hg/hgc/gtexClick.c - lines changed 34, context: html, text, full: html, text
• Preliminary work to add tick marks and sanity check Y axis label (max value) on GTEx expression graph. refs #15645
  
  • src/hg/hgc/gtexClick.c - lines changed 49, context: html, text, full: html, text
• Exploratory use of D3 JS for boxplot on GTEX gene track details page. refs #15645
  
  • src/hg/hgc/gtexClick.c - lines changed 252, context: html, text, full: html, text
  • src/hg/js/makefile - lines changed 4, context: html, text, full: html, text
• Initial code for R-based graph on GTEx details page. refs #15645
  
  • src/hg/hgc/gtex/geneBoxplot.R - lines changed 31, context: html, text, full: html, text
  • src/hg/hgc/gtexClick.c - lines changed 47, context: html, text, full: html, text
• Add X axis labels, rotated 45 degrees. Adjust colors, line styles,e tc. refs #15645
  
  • src/hg/hgc/gtex/geneBoxplot.R - lines changed 35, context: html, text, full: html, text
  • src/hg/hgc/gtexClick.c - lines changed 7, context: html, text, full: html, text
• Scale graph limits and place X axis labels appropriately for variously ranged graphs, and log transformed data. refs #15645
  
  • src/hg/hgc/gtex/geneBoxplot.R - lines changed 29, context: html, text, full: html, text
  • src/hg/hgc/gtexClick.c - lines changed 7, context: html, text, full: html, text
• Colors and labels now reordered propertly. refs #15645
  
  • src/hg/hgc/gtex/geneBoxplot.R - lines changed 11, context: html, text, full: html, text
• Make R graphics default. refs #15645
  
  • src/hg/hgc/gtexClick.c - lines changed 6, context: html, text, full: html, text
• Fix label ordering. This is final check-in before ripping out alternate implementations (JS and C). Will keep this in a branch. refs #15645
  
  • src/hg/hgc/gtex/geneBoxplot.R - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/gtex/2014-jan.txt - lines changed 15, context: html, text, full: html, text
• Checking in graph exploratory work (JS D3) to save it (in a branch) before whacking. refs #15645
  
  • src/hg/hgGtexApi/hgGtexApi.c - lines changed 78, context: html, text, full: html, text
  • src/hg/hgGtexApi/makefile - lines changed 14, context: html, text, full: html, text
  • src/hg/hgc/gtex/tissueColors.R - lines changed 58, context: html, text, full: html, text
  • src/hg/hgc/makefile - lines changed 9, context: html, text, full: html, text
  • src/hg/js/d3.min.js - lines changed 5, context: html, text, full: html, text
  • src/hg/js/d3plus.gtex.js - lines changed 33973, context: html, text, full: html, text
  • src/hg/js/gtex.js - lines changed 18, context: html, text, full: html, text
• Code cleanup in preparation for mergingin into main. refs #15645
  
  • src/hg/hgc/gtex/geneBoxplot.R - lines changed 74, context: html, text, full: html, text
  • src/hg/hgc/gtex/tissueColors.R - lines changed 58, context: html, text, full: html, text
  • src/hg/hgc/gtexClick.c - lines changed 218, context: html, text, full: html, text
  • src/hg/hgc/hgcData/gtexBoxplot.R - lines changed 72, context: html, text, full: html, text
  • src/hg/hgc/hgcData/gtexColorsV4.R - lines changed 58, context: html, text, full: html, text
  • src/hg/hgc/makefile - lines changed 9, context: html, text, full: html, text
  • src/hg/js/d3.min.js - lines changed 5, context: html, text, full: html, text
  • src/hg/js/d3plus.gtex.js - lines changed 33973, context: html, text, full: html, text
  • src/hg/js/gtex.js - lines changed 18, context: html, text, full: html, text
  • src/hg/js/makefile - lines changed 2, context: html, text, full: html, text
• Cleanup trackUi in prep for merging into main. refs #15645
  
  • src/hg/hgTracks/gtexTracks.c - lines changed 4, context: html, text, full: html, text
  • src/hg/inc/gtexUi.h - lines changed 28, context: html, text, full: html, text
  • src/hg/lib/gtexUi.c - lines changed 56, context: html, text, full: html, text
  • src/hg/lib/hui.c - lines changed 59, context: html, text, full: html, text
  • src/hg/lib/makefile - lines changed 1, context: html, text, full: html, text
• Code cleanup, in preparation for branch merge. refs #15645
  
  • src/hg/hgTracks/gtexTracks.c - lines changed 404, context: html, text, full: html, text
• Add map box to comparison graph. Code cleanup. refs #15645
  
  • src/hg/hgTracks/gtexTracks.c - lines changed 146, context: html, text, full: html, text
• Improve display for non-log transformed by adding max view limit. refs #15645
  
  • src/hg/hgTracks/gtexTracks.c - lines changed 43, context: html, text, full: html, text
  • src/hg/inc/gtexUi.h - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/gtexUi.c - lines changed 2, context: html, text, full: html, text
• Backing out JS details page for GTEx
  
  • src/hg/js/makefile - lines changed 2, context: html, text, full: html, text
• Resolving merge
  
  • src/hg/hgTracks/hgTracks.c - lines changed 3, context: html, text, full: html, text
  • src/inc/memgfx.h - lines changed 12, context: html, text, full: html, text
  • src/inc/rainbow.h - lines changed 7, context: html, text, full: html, text
  • src/lib/rainbow.c - lines changed 23, context: html, text, full: html, text
• Fix map boxes on non-log display. refs #15645
  
  • src/hg/hgTracks/gtexTracks.c - lines changed 47, context: html, text, full: html, text
  • src/hg/inc/gtexUi.h - lines changed 1, context: html, text, full: html, text