ba14f4302cf8fb07c94849c27fe1793ddabdbc92 dschmelt Tue Jan 21 12:17:09 2020 -0800 Adding track height URL setting #24794 diff --git src/hg/htdocs/goldenPath/help/customTrackText.html src/hg/htdocs/goldenPath/help/customTrackText.html index fa77b09..74041b0 100755 --- src/hg/htdocs/goldenPath/help/customTrackText.html +++ src/hg/htdocs/goldenPath/help/customTrackText.html @@ -748,30 +748,36 @@ target="_blank">example link</a> to create a 300-pixel wide image</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><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><trackName>.heightPer=<number></code> - sets the height of the a bigWig track + in pixels - <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=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&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 @@ -785,32 +791,32 @@ <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> <p> Combine the above pieces of information into a URL of the following format (the information specific to your annotation file is highlighted):</p> <pre><code>http://genome.ucsc.edu/cgi-bin/hgTracks?org=<font color="000099"><em>organism_name</em></font>&position=<font color="000099"><em>chr_position</em></font>&hgt.customText=<font color="000099"><em>URL</em></font></code></pre> <p> <strong><em>Example #5:</em></strong><br> The following URL will open up the Genome Browser window to display chr22 of the latest human genome assembly and will show the annotation track pointed to by the URL http://genome.ucsc.edu/goldenPath/help/test.bed: <pre><code <a class="insideLink" href="../../cgi-bin/hgTracks?org=human&position=chr22&hgt.customText=http://genome.ucsc.edu/goldenPath/help/test.bed" target="_blank">http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&position=chr22&hgt.customText=http://genome.ucsc.edu/goldenPath/help/test.bed</a></code></pre> <p> -<strong>Step 3.</strong> Provide the URL to others. To upload a custom annotation track pointed to -by a URL into the Genome Browser, paste the URL into the large text edit box on the Add Custom +<strong>Step 3.</strong> Provide the URL to others. To upload a custom annotation track from a +URL into the Genome Browser, paste the URL into the large text edit box on the Add Custom Tracks page, then click the Submit button.</p> <p> If you'd like to share your annotation track with a broader audience, send the URL for your track—along with a description of the format, methods, and data used—to the UCSC Genome mailing list <a href="mailto:genome@soe.ucsc.edu">genome@soe.ucsc.edu</a>. <!-- above address is genome at soe.ucsc.edu --> <a name="EXAMPLE6"></a> <p> <strong><em>Example #6:</em></strong><br> If you would like to share a URL that your colleague can click on directly, rather than loading it in the Custom Track tool (as in Example #5), then the URL will need a few extra parameters. Let's assume that your data is on a server at your institution in one of the large data formats: <a href="../../FAQ/FAQformat.html#format1.5">bigBed</a>,