220420c493c9dd3d509cd6fb6084b3bf756d8ef4 dschmelt Fri May 24 12:09:02 2019 -0700 Making b0b's CR changes #23528 diff --git src/hg/htdocs/goldenPath/help/customTrackText.html src/hg/htdocs/goldenPath/help/customTrackText.html index 50458bf..0b130d8 100755 --- src/hg/htdocs/goldenPath/help/customTrackText.html +++ src/hg/htdocs/goldenPath/help/customTrackText.html @@ -679,122 +679,101 @@ or without a set of coordinates. Examples of this include: position=chr22, position=chr22:15916196-31832390.</li> <li> The URL of the annotation file on your web site. This information is of the form <code>hgt.customText=URL</code>, where <em>URL</em> points to the annotation file on your website. An example of an annotation file URL is <a href="test.bed" target="_blank">http://genome.ucsc.edu/goldenPath/help/test.bed</a>.</li> </ul> <a name="optParams"></a> <p> 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.) <ul> <li> - <code>ignoreCookie=1</code> - uses default user settings like track selections, custom -tracks, and track hubs - <a href="../../cgi-bin/hgTracks?db=hg19&ignoreCookie=1" - target="_blank">example link</a> to show the default tracks and positions for hg19</li> + <code>guidelines=on/off</code> - activate or deactivate the blue guidelines - + <a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&guidelines=off" + target="_blank">example link</a> to switch off blue guidelines</li> <li> <code>hgFind.matches=listOfNames</code> - highlight features given their names - <a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&hgFind.matches=uc010naf.1,uc011mcz.1" target="_blank">example link</a> to highlight two transcripts of the ABO gene</li> <li> - <code><trackName>=full|dense|pack|hide</code> - show the default tracks adding a track and - set it to full, dense, pack or hide visibility - - <a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&cytoBand=pack" - target="_blank">example link</a> 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 - <code>ct_name_####</code>, only with the full custom track name will this feature work: - <code>ct_name_####=full</code></li> + <code>hgt.reset=1</code> - show only the default tracks - + <a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&hgt.reset=1" + target="_blank" >example link</a></li> + <li> + <code>hgt.toggleRevCmplDisp=1</code> - show the reverse-complement - + <a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&hgt.toggleRevCmplDisp=1" + target="_blank">example link</a> to show the reverse-complement of the ABO gene</li> + <li> + <code>hgt.labelWidth=<number></code> - set the size of the left-side label area - + <a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&hgt.labelWidth=50" + target="_blank">example link</a> to increase the label area to 50 characters</li> <li> <code>hideTracks=1</code> - hide all tracks - <a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&hideTracks=1" target="_blank">example link</a> to show no tracks at all</li> <li> <code>hideTracks=1&<trackName>=full|dense|pack|hide</code> - hide all tracks and show other tracks - <a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&hideTracks=1&cytoBand=pack" target="_blank">example link</a> to show only the Chromosome Bands track and nothing else</li> <li> - <code><trackName>_hideKids=1</code> - hides a specific super track's individual tracks - <a - href="../../cgi-bin/hgTracks?db=hg19&wgEncodeReg_hideKids=1&ignoreCookie=1" target="_blank"> - example link</a> to hide the Encode Regulation super track</li> - <li> - <code><trackName>_sel=1</code> - selects specific subtrack to be 'checked', allowing - display - <a href="../../cgi-bin/hgTracks?db=hg38&refGene_sel=1" target="_blank">example - link</a> to select the checkbox for UCSC refSeq in the refSeq composite track, allowing display - alongside default tracks - </li> - <li> - <code>hgt.reset=1</code> - show only the default tracks - - <a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&hgt.reset=1" - target="_blank" >example link</a></li> - <li> - <code>hgt.toggleRevCmplDisp=1</code> - show the reverse-complement - - <a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&hgt.toggleRevCmplDisp=1" - target="_blank">example link</a> to show the reverse-complement of the ABO gene</li> - <li> - <code>oligoMatch=pack&hgt.oligoMatch=DNASEQ</code> - switch on the Short Match track and - highlight a matching sequence - - <a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&oligoMatch=pack&hgt.oligoMatch=TATAWAR" - target="_blank">example link</a> to highlight the TATAWAR motif in the ABO locus</li> - <li> <code>highlight=<DB>.<CHROM>:<START>-<END>#<COLOR>|...</code> - highlight one or more regions in a given color on the image. Note that the arguments have to be URL-encoded for Internet browsers, so ":" becomes "%3A", "#" becomes "%23" and "|" becomes "%7"C. - <a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136136597-136139844&highlight=hg19.chr9%3A136138630-136139650%23AA0000%7Chg19.chr9%3A136136630-136137650%230000FF" target="_blank">example link</a> to highlight two parts of the ABO locus in red and blue.</li> <li> + <code>ignoreCookie=1</code> - uses default user settings like track selections, custom + tracks, and track hubs - <a href="../../cgi-bin/hgTracks?db=hg19&ignoreCookie=1" + target="_blank">example link</a> to show the default tracks and positions for hg19</li> + <li> + <code>oligoMatch=pack&hgt.oligoMatch=DNASEQ</code> - switch on the Short Match track and + highlight a matching sequence - + <a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&oligoMatch=pack&hgt.oligoMatch=TATAWAR" + target="_blank">example link</a> to highlight the TATAWAR motif in the ABO locus</li> + <li> <code>pix=<number></code> - set the width of the image in pixels - <a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&pix=300" target="_blank">example link</a> to create a 300-pixel wide image</li> <li> - <code>hgt.labelWidth=<number></code> - set the size of the left-side label area - - <a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&hgt.labelWidth=50" - target="_blank">example link</a> to increase the label area to 50 characters</li> - <li> <code>textSize=<number></code> - set the size of text font - <a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&textSize=12" target="_blank">example link</a> to increase the text font size to 12 pixels</li> <li> - <code>guidelines=on/off</code> - activate or deactivate the blue guidelines - - <a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&guidelines=off" - target="_blank">example link</a> to switch off blue guidelines</li> - - <li> - <code>enableHighlightingDialog=0/1</code> - activate or deactivate the highlighting/zoom - dialog - <a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&enableHighlightingDialog=0" - target="_blank">example link</a> to default to zoom mode and switch off the highlight - dialog</li> - + <code><trackName>=full|dense|pack|hide</code> - show the default tracks adding a track and + set it to full, dense, pack or hide visibility - + <a href="../../cgi-bin/hgTracks?db=hg19&position=chr9%3A136130563-136150630&cytoBand=pack" + target="_blank">example link</a> 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 + <code>ct_name_####</code>, only with the full custom track name will this feature work: + <code>ct_name_####=full</code></li> <li> - <code>position=<geneSymbol>&singleSearch=knownCanonical</code> - - Jump directly to the location of a gene, without showing the search results - - <a href="../../cgi-bin/hgTracks?db=hg19&position=PITX2&singleSearch=knownCanonical" - target="_blank">example link</a> to jump directly to the PITX2 gene on hg19 - dialog</li> - + <code><trackName>_hideKids=1</code> - hides a specific super track's individual tracks - <a + href="../../cgi-bin/hgTracks?db=hg19&wgEncodeReg_hideKids=1&ignoreCookie=1" target="_blank"> + example link</a> to hide the Encode Regulation super track</li> <li> - <code>position=<rsID>&singleSearch=snp150</code> - - Jump directly to the first search result of the specified query on the declared track - - <a href="../../cgi-bin/hgTracks?db=hg38&position=rs104894977&singleSearch=snp150" - target="_blank">example link</a> to go directly to the top rs10489494977 id hit of the snp150 - track on hg38</li> - + <code><trackName>_sel=1</code> - selects specific subtrack to be 'checked', allowing + display - <a href="../../cgi-bin/hgTracks?db=hg38&refSeqComposite=full&refGene_sel=1" target="_blank">example + link</a> to select the checkbox for UCSC RefSeq subtrack in the refSeq composite track, allowing + display alongside default tracks + </li> </ul> <p> If a login and password is required to access data loaded through a URL (e.g., via https: protocol), this information can be included in the URL using the format protocol://user:password@server.com/somepath. Only Basic Authentication is supported for HTTP. Note that passwords included in URLs are not protected. If a password contains a non-alphanumeric character, such as $, the character must be replaced by the hexadecimal representation for that character. For example, in the password mypwd$wk, the $ character should be replaced by %24, resulting in the modified password mypwd%24wk.</p> <p> For integration into your own website e.g. in an html IFRAME, you can obtain the track image only, without the rest of the genome browser user interface, by replacing hgTracks in the URL with hgRenderTracks, like in this example:</p> <pre><code><a href="http://genome.ucsc.edu/cgi-bin/hgRenderTracks?db=hg19&position=chr9%3A136130563-136150630" target="_blank">http://genome.ucsc.edu/cgi-bin/hgRenderTracks?db=hg19&position=chr9%3A136130563-136150630</a></code></pre>