5c20012735003a09af722339a7ea57f5cb827066 dschmelt Mon May 13 14:59:08 2019 -0700 Commiting minor changes for code review #23486, also adding more param lines to customTrack text #23459 diff --git src/hg/htdocs/goldenPath/help/customTrackText.html src/hg/htdocs/goldenPath/help/customTrackText.html index 922a4d9..011db3b 100755 --- src/hg/htdocs/goldenPath/help/customTrackText.html +++ src/hg/htdocs/goldenPath/help/customTrackText.html @@ -555,30 +555,31 @@

itemRgb=On - If this attribute is present and is set to "On", the Genome Browser will use the RGB value shown in the itemRgb field in each data line of the associated BED track to determine the display color of the data on that line.

colorByStrand=<RRR,GGG,BBB RRR,GGG,BBB> - Sets colors for + and - strands, in that order. The colors consist of three comma-separated RGB values from 0-255 each. The default is 0,0,0 0,0,0 (both black).

+ useScore=<use_score> - If this attribute is present and is set to 1, the score field in each of the track's data lines will be used to determine the level of shading in which the data is displayed. The track will display in shades of gray unless the color attribute is set to 100,50,0 (shades of brown) or 0,60,120 (shades of blue). The default setting for useScore is "0". This table shows the Genome Browser's translation of BED score values into shades of gray:

@@ -679,52 +680,66 @@ or without a set of coordinates. Examples of this include: position=chr22, position=chr22:15916196-31832390.

The URL of the annotation file on your web site. This information is of the form hgt.customText=URL, where URL points to the annotation file on your website. An example of an annotation file URL is http://genome.ucsc.edu/goldenPath/help/test.bed.

You can add other optional parameters to the URL: (Note: Display may vary if you have conflicting cart variables, for example having both hide all and highlight features.)

+ ignoreCookie=1 - uses default user settings like track selections, custom +tracks, and track hubs - example link to show the default tracks and positions for hg19
hgFind.matches=listOfNames - highlight features given their names - example link to highlight two transcripts of the ABO gene
<trackName>=full|dense|pack|hide - show the default tracks adding a track and set it to full, dense, pack or hide visibility - example link to show the default or user-selected tracks and set the Chromosome Bands track to "pack" view. Please note that for this feature to work with custom tracks you must use their unique assigned name and identifier number ct_name_####, only with the full custom track name will this feature work: ct_name_####=full
hideTracks=1 - hide all tracks - example link to show no tracks at all
hideTracks=1&<trackName>=full|dense|pack|hide - hide all tracks and show other tracks - example link to show only the Chromosome Bands track and nothing else
+ <trackName>_hideKids=1 - hides a specific super track's individual tracks - + example link to hide the Encode Regulation super track
+ <trackName>_sel=1 - selects specific subtrack to be 'checked', allowing + display - example + link to select the checkbox for UCSC refSeq in the refSeq composite track, allowing display + alongside default tracks +
hgt.reset=1 - show only the default tracks - example link
hgt.toggleRevCmplDisp=1 - show the reverse-complement - example link to show the reverse-complement of the ABO gene
oligoMatch=pack&hgt.oligoMatch=DNASEQ - switch on the Short Match track and highlight a matching sequence - example link to highlight the TATAWAR motif in the ABO locus
highlight=<DB>.<CHROM>:<START>-<END>#<COLOR>|... - highlight one or more regions in a given color on the image. Note that the arguments have to be

shade