File Changes for kate

v330_base to v331_preview (2016-03-21 to 2016-03-28) v331

• src/hg/hgTracks/gtexTracks.c
  • lines changed 24, context: html, text, full: html, text
    Add checkbox to limit to protein coding genes (I keep wanting this option during testing.). refs #15645
    
  • lines changed 78, context: html, text, full: html, text
    1. Add -log option to bedScore. 2. Score GTEx gene track bed files based on total median expression level across all tissues, for use in dense mode (gray-scale based on total expression), and display score on details page. 3. Implement viz for squished mode -- show color of highest expressed tissue if over threshold, and show tissue name in mouseover. refs #15645
    
  • lines changed 3, context: html, text, full: html, text
    Remove debug statements.
    
• src/hg/hgc/gtexClick.c
  • lines changed 2, context: html, text, full: html, text
    Indicate assembly next to genomic position on item details. refs #15645
    
  • lines changed 1, context: html, text, full: html, text
    Add version awareness to tissue handling. refs #15645
    
  • lines changed 8, context: html, text, full: html, text
    Readability improvements to gene details page boxplot. Use long labels instead of short. Space out sample counts. Change yellow text to black. refs #15645
    
  • lines changed 2, context: html, text, full: html, text
    1. Add -log option to bedScore. 2. Score GTEx gene track bed files based on total median expression level across all tissues, for use in dense mode (gray-scale based on total expression), and display score on details page. 3. Implement viz for squished mode -- show color of highest expressed tissue if over threshold, and show tissue name in mouseover. refs #15645
    
• src/hg/hgc/hgcData/gtexBoxplot.R
  • lines changed 7, context: html, text, full: html, text
    Readability improvements to gene details page boxplot. Use long labels instead of short. Space out sample counts. Change yellow text to black. refs #15645
    
• src/hg/hgc/hgcData/gtexColorsV4.R
  • lines changed 64, context: html, text, full: html, text
    Readability improvements to gene details page boxplot. Use long labels instead of short. Space out sample counts. Change yellow text to black. refs #15645
    
  • lines changed 4, context: html, text, full: html, text
    Fix swapped colors.
    
• src/hg/htdocs/images/gtex/gtexGeneTcap.png
  • lines changed 0, context: html, text, full: html, text
    Create plots for V6 sample characterization and add images to track description page. refs #15645
    
• src/hg/htdocs/images/gtex/gtexSampleAge.V6.png
  • lines changed 0, context: html, text, full: html, text
    Create plots for V6 sample characterization and add images to track description page. refs #15645
    
• src/hg/htdocs/images/gtex/gtexSampleRin.V6.png
  • lines changed 0, context: html, text, full: html, text
    Create plots for V6 sample characterization and add images to track description page. refs #15645
    
• src/hg/htdocs/images/gtexGeneTcap.png
  • lines changed 0, context: html, text, full: html, text
    Create plots for V6 sample characterization and add images to track description page. refs #15645
    
• src/hg/inc/gtexGeneBed.h
  • lines changed 3, context: html, text, full: html, text
    Add checkbox to limit to protein coding genes (I keep wanting this option during testing.). refs #15645
    
• src/hg/inc/gtexInfo.h
  • lines changed 3, context: html, text, full: html, text
    Add version awareness to tissue handling. refs #15645
    
• src/hg/inc/gtexTissue.h
  • lines changed 2, context: html, text, full: html, text
    Add version awareness to tissue handling. refs #15645
    
• src/hg/inc/gtexUi.h
  • lines changed 4, context: html, text, full: html, text
    Add checkbox to limit to protein coding genes (I keep wanting this option during testing.). refs #15645
    
• src/hg/lib/gtexGeneBed.c
  • lines changed 8, context: html, text, full: html, text
    Add version awareness to tissue handling. refs #15645
    
  • lines changed 5, context: html, text, full: html, text
    Add checkbox to limit to protein coding genes (I keep wanting this option during testing.). refs #15645
    
• src/hg/lib/gtexGeneBed.sql
  • lines changed 2, context: html, text, full: html, text
    1. Add -log option to bedScore. 2. Score GTEx gene track bed files based on total median expression level across all tissues, for use in dense mode (gray-scale based on total expression), and display score on details page. 3. Implement viz for squished mode -- show color of highest expressed tissue if over threshold, and show tissue name in mouseover. refs #15645
    
• src/hg/lib/gtexInfo.c
  • lines changed 8, context: html, text, full: html, text
    Add version awareness to tissue handling. refs #15645
    
• src/hg/lib/gtexTissue.c
  • lines changed 7, context: html, text, full: html, text
    Add version awareness to tissue handling. refs #15645
    
• src/hg/lib/gtexUi.c
  • lines changed 4, context: html, text, full: html, text
    Add version awareness to tissue handling. refs #15645
    
  • lines changed 7, context: html, text, full: html, text
    Add checkbox to limit to protein coding genes (I keep wanting this option during testing.). refs #15645
    
• src/hg/makeDb/doc/gtex/V6.txt
  • lines changed 30, context: html, text, full: html, text
    Reloaded gtexSampleData to restore zero-valued rows so details page boxplot has all data (o/w need special code for missing data). Extend parser to create median tables by gender to speed up gender diffs feature (changes also needed to hgGtexGeneBed and hgTracks to use these). refs #15645
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 54, context: html, text, full: html, text
    1. Add -log option to bedScore. 2. Score GTEx gene track bed files based on total median expression level across all tissues, for use in dense mode (gray-scale based on total expression), and display score on details page. 3. Implement viz for squished mode -- show color of highest expressed tissue if over threshold, and show tissue name in mouseover. refs #15645
    
• src/hg/makeDb/doc/hg38/gtex.txt
  • lines changed 45, context: html, text, full: html, text
    1. Add -log option to bedScore. 2. Score GTEx gene track bed files based on total median expression level across all tissues, for use in dense mode (gray-scale based on total expression), and display score on details page. 3. Implement viz for squished mode -- show color of highest expressed tissue if over threshold, and show tissue name in mouseover. refs #15645
    
• src/hg/makeDb/outside/gtexPlot/README.txt
  • lines changed 16, context: html, text, full: html, text
    Create plots for V6 sample characterization and add images to track description page. refs #15645
    
• src/hg/makeDb/outside/gtexPlot/makeSampleDf.csh
  • lines changed 2, context: html, text, full: html, text
    Create plots for V6 sample characterization and add images to track description page. refs #15645
    
• src/hg/makeDb/outside/gtexPlot/plotSampleAge.R
  • lines changed 54, context: html, text, full: html, text
    Create plots for V6 sample characterization and add images to track description page. refs #15645
    
• src/hg/makeDb/outside/gtexPlot/plotSampleRin.R
  • lines changed 43, context: html, text, full: html, text
    Create plots for V6 sample characterization and add images to track description page. refs #15645
    
• src/hg/makeDb/outside/hgGtex/hgGtex.c
  • lines changed 255, context: html, text, full: html, text
    Reloaded gtexSampleData to restore zero-valued rows so details page boxplot has all data (o/w need special code for missing data). Extend parser to create median tables by gender to speed up gender diffs feature (changes also needed to hgGtexGeneBed and hgTracks to use these). refs #15645
    
• src/hg/makeDb/outside/hgGtexExonBed/hgGtexExonBed.c
  • lines changed 8, context: html, text, full: html, text
    Fix compile err.
    
• src/hg/makeDb/outside/hgGtexGeneBed/hgGtexGeneBed.c
  • lines changed 8, context: html, text, full: html, text
    Fix compile err.
    
• src/hg/makeDb/trackDb/human/gtexGeneExpr.html
  • lines changed 5, context: html, text, full: html, text
    Create plots for V6 sample characterization and add images to track description page. refs #15645
    
  • lines changed 1, context: html, text, full: html, text
    Minor wording change.
    
• src/hg/makeDb/trackDb/human/trackDb.gtex.ra
  • lines changed 1, context: html, text, full: html, text
    1. Add -log option to bedScore. 2. Score GTEx gene track bed files based on total median expression level across all tissues, for use in dense mode (gray-scale based on total expression), and display score on details page. 3. Implement viz for squished mode -- show color of highest expressed tissue if over threshold, and show tissue name in mouseover. refs #15645
    
• src/inc/sqlList.h
  • lines changed 3, context: html, text, full: html, text
    1. Add -log option to bedScore. 2. Score GTEx gene track bed files based on total median expression level across all tissues, for use in dense mode (gray-scale based on total expression), and display score on details page. 3. Implement viz for squished mode -- show color of highest expressed tissue if over threshold, and show tissue name in mouseover. refs #15645
    
• src/lib/sqlList.c
  • lines changed 20, context: html, text, full: html, text
    1. Add -log option to bedScore. 2. Score GTEx gene track bed files based on total median expression level across all tissues, for use in dense mode (gray-scale based on total expression), and display score on details page. 3. Implement viz for squished mode -- show color of highest expressed tissue if over threshold, and show tissue name in mouseover. refs #15645
    
• src/lib/tests/makefile
  • lines changed 4, context: html, text, full: html, text
    1. Add -log option to bedScore. 2. Score GTEx gene track bed files based on total median expression level across all tissues, for use in dense mode (gray-scale based on total expression), and display score on details page. 3. Implement viz for squished mode -- show color of highest expressed tissue if over threshold, and show tissue name in mouseover. refs #15645
    
• src/lib/tests/testSum.c
  • lines changed 35, context: html, text, full: html, text
    1. Add -log option to bedScore. 2. Score GTEx gene track bed files based on total median expression level across all tissues, for use in dense mode (gray-scale based on total expression), and display score on details page. 3. Implement viz for squished mode -- show color of highest expressed tissue if over threshold, and show tissue name in mouseover. refs #15645
    
• src/utils/bedScore/bedScore.c
  • lines changed 16, context: html, text, full: html, text
    1. Add -log option to bedScore. 2. Score GTEx gene track bed files based on total median expression level across all tissues, for use in dense mode (gray-scale based on total expression), and display score on details page. 3. Implement viz for squished mode -- show color of highest expressed tissue if over threshold, and show tissue name in mouseover. refs #15645