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diff --git a/web/heatmap.html b/web/heatmap.html new file mode 100755 index 00000000..b1b726e7 --- /dev/null +++ b/web/heatmap.html @@ -0,0 +1,64 @@ +<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"> +<HTML><HEAD><TITLE>QTL heatmap</TITLE> +<META http-equiv=Content-Type content="text/html; charset=iso-8859-1"> +<LINK REL="stylesheet" TYPE="text/css" HREF='css/general.css'> +<LINK REL="stylesheet" TYPE="text/css" HREF='css/menu.css'> +<SCRIPT SRC="javascript/webqtl.js"></SCRIPT> + + +</HEAD> +<BODY bottommargin="2" leftmargin="2" rightmargin="2" topmargin="2" text=#000000 bgColor=#ffffff> +<TABLE cellSpacing=5 cellPadding=4 width="100%" border=0> + <TBODY> + <TR> + <script language="JavaScript" src="/javascript/header.js"></script> + </TR> + <TR> + <TD bgColor=#eeeeee class="solidBorder"> + <Table width= "100%" cellSpacing=0 cellPadding=5><TR> + <!-- Body Start from Here --> + <TD valign="top" height="200" width="100%" bgcolor="#eeeeee"> + + <P class="title">What is QTL heatmap? <A HREF="/webqtl/main.py?FormID=editHtml"><img src="images/modify.gif" alt="modify this page" border= 0 valign="middle"></A></P> + +<Blockquote> +The upper part of this page includes a hierarchical cluster tree of the set of traits you selected in the previous window. To generate this plot, we initially compute distances between pairs of traits using (1 - r) where r is the Pearson product-moment correlation. The hierarchy is assembled by successively linking traits and groups of traits. +<P></P> +The lower part of this page provides a QTL heat map for all members of the Cluster Tree, extending from proximal Chr 1 at the top to distal Chr X at the bottom. Each vertical column or stripe encodes the genome-wide p value computed on the basis of 1000 permutations. Orange triangles mark the approximate location of genes. +<P></P> +These QTL heat maps can be redrawn using alternative color assignments using the "Redraw Cluster Tree" option. The default heat map is "Grey + Blue + Red" in which more intense colors mark chromosomal regions with comparatively high linkage statistics and the spectrum encodes the allelic effect. For example, blue-green regions are those in which one of the parental alleles (e.g., C57BL/6J) is associated with higher trait values, whereas red-yellow regions are those in which the other parental allele is associated with higher trait values. Grey and black regions have insignfiicant linkage to trait variance. The "Blue + Red" option is similar but the entire genome is encoded for allele polarity, including regions without significant linkage. Finally, " Single Spectrum" provides a plot that does not distinguish between allelic effects and encodes the p values, ranging from insignificant (dark blue) to genome-wide significant (bright red). +<P></P> +</Blockquote> + +<P></P> + </TD> + </TR></TABLE> + </TD> + </TR> + <TR> + <TD align=center bgColor=#ddddff class="solidBorder"> + <!--Start of footer--> + <TABLE width="90%"> + <script language='JavaScript' src='/javascript/footer.js'></script> + </TABLE> + <!--End of footer--> + </TD> + </TR> +</TABLE> +<!-- /Footer --> +<script language="JavaScript" src="/javascript/menu_new.js"></script> +<script language="JavaScript" src="/javascript/menu_items.js"></script> +<script language="JavaScript" src="/javascript/menu_tpl.js"></script> +<script language="JavaScript"> + <!--// + new menu (MENU_ITEMS, MENU_POS); + //--> +</script> +<script src="http://www.google-analytics.com/urchin.js" type="text/javascript"> +</script> +<script type="text/javascript"> +_uacct = "UA-3782271-1"; +urchinTracker(); +</script> +</BODY> +</HTML> |