328e57766a279798e1c9f370da17badb7cd16f6d dschmelt Tue Nov 12 16:52:57 2019 -0800 Minor proofread edits to Jonathan's Hic docs #22316 diff --git src/hg/htdocs/goldenPath/help/hgHicTrackHelp.html src/hg/htdocs/goldenPath/help/hgHicTrackHelp.html index c626f78..ae7c03c 100755 --- src/hg/htdocs/goldenPath/help/hgHicTrackHelp.html +++ src/hg/htdocs/goldenPath/help/hgHicTrackHelp.html @@ -1,46 +1,47 @@ <!DOCTYPE html> <!--#set var="TITLE" value="Genome Browser hic Tracks" --> <!--#set var="ROOT" value="../.." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <!-- hic Track Help Page --> <h1>Configuring hic tracks</h1> <p> -Genome Browser hic tracks display heatmaps of chromatin folding data, and may be configured +Genome Browser hic tracks display heatmaps of chromatin folding data and may be configured in several ways to highlight different aspects of the data. By default, hic tracks will use auto-scale options for resolution and score coloring. </p> <p> The following section describes configuration settings available to hic tracks. For more information on setting up and uploading hic data, click the link on <a href="hic.html" target="_blank"> hic custom track creation</a>. </p> <h2>Configuring the display mode</h2> <p> There are three display methods available for Hi-C heatmaps: square, triangle, and arc. <p class='text-center'> <img src="../../images/hicDrawModes.png" alt="hic draw modes"> </p> <p> Square mode provides a traditional Hi-C display in which chromosome positions are mapped along the -top-left-to-bottom-right diagonal, and interaction values are plotted on both sides of that diagonal -to form a square. The upper-left corner of the square corresponds to the left-most position of the -window in view, while the bottom-right corner corresponds to the right-most position of the window. +top-left-to-bottom-right diagonal. Interaction values are plotted symetrically on both sides of +that diagonal to form a square. The upper-left corner of the square corresponds to the left-most +position of the window in view, while the bottom-right corner corresponds to the right-most +position of the window. </p><p> The color shade at any point within the square shows the proximity score for two genomic regions: the region where a vertical line drawn from that point intersects with the diagonal, and the region where a horizontal line from that point intersects with the diagonal. A point directly on the diagonal shows the score for how proximal a region is to itself (scores on the diagonal are usually quite high unless no data are available). A point at the extreme bottom left of the square shows the score for how proximal the left-most position within the window is to the right-most position within the window. </p><p> In triangle mode, the display is quite similar to square except that only the top half of the square is drawn (eliminating the redundancy), and the image is rotated so that the diagonal of the square now lies on the horizontal axis. This display consumes less vertical space in the image, although it may be more difficult to ascertain exactly which positions correspond to a point within the triangle. </p><p>