837fb9fdc2e3db16abf0c91e3382acc7e3b84191 gperez2 Thu Mar 28 12:39:08 2024 -0700 Added optional URL parameters from customTrack.html#SHARE, updated them for hg38, and added them to FAQlink.html#trackViz, refs #30575 diff --git src/hg/htdocs/FAQ/FAQlink.html src/hg/htdocs/FAQ/FAQlink.html index cf7d2fe..aaf55a7 100755 --- src/hg/htdocs/FAQ/FAQlink.html +++ src/hg/htdocs/FAQ/FAQlink.html @@ -150,43 +150,130 @@ <li id="hgt.out3"><code>hgt.out3=submit</code> zooms out 10x</li> <li id="hgt.out4"><code>hgt.out4=submit</code> zooms out 100x</li> </ul> <p> The following link is an example which leads to the variant NM_00257:c.1208G>T and zooms out 3x:</p> <p> <code><a href="../cgi-bin/hgTracks?db=hg19&position=NM_000257:c.1208G%3ET&hgt.out2=submit">http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=NM_000257:c.1208G>T&hgt.out2=submit</a></code></p> <a name="trackViz"></a> <h2>Setting Track Visibility via URL</h2> <h6>How do I create a custom URL to control the visibility of specific tracks?</h6> <p> You can control the visibility of tracks from the URL with the following parameters, -each linked by the "&" sign, similar to position parameters. For more information, please see -the <a href="../goldenPath/help/customTrack.html#optParams" target ="_blank">optional URL -parameters</a> section of the Custom Tracks User's Guide.</p> +each linked by the "&" sign: <ul> -<li id="hideTracks"><code>hideTracks=1</code> - hides all tracks</li> -<li><code><trackName>=hide|dense|pack|full</code> - sets specified track or subtrack to a -chosen visibility</li> -<li id="textSize"><code>textSize=<number></code> - sets browser text size to either 6, 8, 10, 12, 14, 18, -24, or 34. Default is a textSize of 12.</li> -<li><code><trackName>.heightPer=<###></code> - sets a bigWig track's height to a -particular number of pixels (between 20-100)</li> -<li id="ignoreCookie"><code>ignoreCookie=1</code> - removes pre-existing user settings like track selection, custom -tracks, and track hubs</li> + <li> + <code>guidelines=on/off</code> - activate or deactivate the blue guidelines - + <a href="../../cgi-bin/hgTracks?db=hg38&position=chr9%3A133255176-133275214&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=hg38&position=chr9%3A133255176-133275214&hgFind.matches=ENST00000611156.4,ENST00000538324.2" + target="_blank">example link</a> to highlight two transcripts of the ABO gene</li> + <li> + <code>hgt.reset=1</code> - show only the default tracks - + <a href="../../cgi-bin/hgTracks?db=hg38&position=chr9%3A133255176-133275214&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=hg38&position=chr9%3A133255176-133275214&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=hg38&position=chr9%3A133255176-133275214&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=hg38&position=chr9%3A133255176-133275214&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=hg38&position=chr9%3A133255176-133275214&hideTracks=1&cytoBand=pack" + target="_blank">example link</a> to show only the Chromosome Bands track and nothing else</li> + <li> + <code>highlight=<db>.<chrom>:<chromStart>-<chromEnd>#<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=hg38&position=chr9%3A133255176-133275214&highlight=hg38.chr9%3A133255612-133262185%23AA0000%7Chg38.chr9%3A133269124-133274224%230000FF" + target="_blank">example link</a> to highlight two parts of the ABO locus in red and blue.</li> + <li> + <code>ignoreCookie=1</code> - do not load the user's existing settings saved + in the internet browser's UCSC Genome Browser cookie. This means that the link will show the + Genome Browser default + settings such as track selections, custom tracks, and track hubs. Any changes + you make in this new session will, however, affect the user's settings. E.g., + if you add a track in this new window, and come back to the genome browser + later, the track will still be there. This setting is useful if a website + wants to link to the Genome Browser, starting with a "clean slate" but + believes the user will come back to the Genome Browser expecting the + changes to still be there. </li> + <li> + <code>ruler=hide</code> - hide the ruler at the top of the browser image - + <a href="../../cgi-bin/hgTracks?db=hg38&hideTracks=1&knownGene_imgOrd=2&knownGene=pack>exGeneV8=full>exGeneV8_imgOrd=1&ruler=hide" + target="_blank">example link</a> to hide the ruler</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=hg38&position=chr7%3A155796193-155816207&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=hg38&position=chr9%3A133255176-133275214&pix=300" + target="_blank">example link</a> to create a 300-pixel wide image</li> + <li> + <code>textSize=<number></code> - sets browser text size to either 6, 8, 10, 12, 14, 18, 24, + or 34. Default is a textSize of 12. - + <a href="../../cgi-bin/hgTracks?db=hg38&position=chr9%3A133255176-133275214&textSize=18" + target="_blank">example link</a> to increase the text font size to 18 pixels</li> + <li> + <code><trackName>=full|pack|dense|hide</code> - sets specified track or subtrack to a + chosen visibility: full, pack, dense, or hide track - + <a href="../../cgi-bin/hgTracks?db=hg38&position=chr9%3A133255176-133275214&cytoBand=pack" + target="_blank">example link</a> to show the + Chromosome Bands track set to "pack" and added to your view as saved in your cart. + Please note that for this feature to work with + custom tracks you must use the unique name and identifier number + <code>ct_name_####</code> assigned by our system. You can determine the name for a custom track + using the url, <a href = "https://genome.ucsc.edu/cgi-bin/cartDump"> + https://genome.ucsc.edu/cgi-bin/cartDump</a>. + <li> + <code><trackName>_imgOrd=<number></code> - vertically orders the tracks on the image + based on the numbers provided. You need to specify an order for every visible track when using this + parameter - + <a href="../../cgi-bin/hgTracks?db=hg38&hideTracks=1&knownGene_imgOrd=2&knownGene=pack>exGeneV8=full>exGeneV8_imgOrd=1" + target="_blank">example link</a> to show two show knownGene track being listed second with gtex first</li> + <li> + <code><trackName>.heightPer=<number></code> - sets a bigWig track's height to a + particular number of pixels (between 20-100) - + <a href="../../cgi-bin/hgTracks?db=hg38&ignoreCookie=1&hideTracks=1&mappability=full&umap24Quantitative.heightPer=100" + target="_blank">example link</a> to set umap bigWig track height to 100 pixels + </li> + <li> + <code><trackName>_hideKids=1</code> - hides a specific super track's individual tracks - <a + href="../../cgi-bin/hgTracks?db=hg38&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&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> For example, you can use the following command to hide every track (hideTracks=1), set the genome database to hg38 (db=hg38), set the mappability track to full visibility (mappability=full), and set the umap track height to 100 pixels (umap24Quantitative.heightPer=100). Each of these parameters can be used individually or in combination.</p> <p><code><a href="../cgi-bin/hgTracks?db=hg38&ignoreCookie=1&hideTracks=1&mappability=full&umap24Quantitative.heightPer=100"> http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hideTracks=1&mappability=full&umap24Quantitative.heightPer=100</a></code></p> <p>Composite tracks have additional URL parameters that encode options to hide, select, and display subtracks.</p> <ul> <li><code><trackName>_hideKids=1</code> - hides a specific composite track's subtracks</li> <li><code><trackName>_sel=1</code> - selects specific subtrack to be 'checked', allowing