aboutsummaryrefslogtreecommitdiff
path: root/web/heatmap.html
diff options
context:
space:
mode:
Diffstat (limited to 'web/heatmap.html')
-rwxr-xr-xweb/heatmap.html64
1 files changed, 0 insertions, 64 deletions
diff --git a/web/heatmap.html b/web/heatmap.html
deleted file mode 100755
index b1b726e7..00000000
--- a/web/heatmap.html
+++ /dev/null
@@ -1,64 +0,0 @@
-<!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>