diff --git a/docs/menus.sgml b/docs/menus.sgml
index 3415e57556730c9631e7ae71117470d1db285e95..815a44f32b2a80d5d2c11912ab52588d00defa7d 100644
--- a/docs/menus.sgml
+++ b/docs/menus.sgml
@@ -1545,7 +1545,7 @@ GUG 8.3( 12422) GCG 5.3( 8011) GAG 21.3( 31979) GGG 4.3( 6497)
&prog; is able to display some types of user data in a graph that looks like
the GC content graph (see <XREF LINKEND="GRAPHMENU-GC-CONTENT">). This menu
item will prompt the user for the name of a data file which should contain one
-of two possible graph file formats:
+of four possible graph file formats:
</PARA>
<ORDEREDLIST ID="GRAPH-FORMAT">
@@ -1572,11 +1572,14 @@ of two possible graph file formats:
<PARA>
the first column corresponds to the base position and is an integer.
Note to distinguish this format from the previous format the first
- line of the file must start with a '#'. The next column(s) are the data
+ line of the file must start with a '#'. Line colours can be specified
+ in the header using the keyword colour followed by space separated
+ R:G:B values for each line. The next rows(s) are the data
values. Example extract:
<SYNOPSIS>
# BASE VAL1 VAL2 VAL3 VAL4 VAL5 VAL6
+# colour 5:150:55 255:0:0 0:255:0 0:0:255 100:100:100 50:150:50
176 2204.8 848.23 0 0 0 536.04
278 804.99 0 837.2 0 681.63 0
452 0 699.98 0 0 0 251.18
@@ -1589,6 +1592,49 @@ of two possible graph file formats:
</PARA>
</LISTITEM>
+ <LISTITEM ID="GRAPH-FORMAT-3">
+ <PARA>
+ the next two formats are types of <ULINK
+ URL="https://cgwb.nci.nih.gov/goldenPath/help/wiggle.html" TYPE="external">
+ Wiggle formats</ULINK>. The first is variableStep. Note that &prog; only supports
+ the colour element in the track line.
+ </PARA>
+<SYNOPSIS>
+track type=wiggle_0 color=255,200,0
+variableStep chrom=chr19 span=10
+310 1
+320 12
+330 18
+340 6
+350 5
+430 3
+440 1
+</SYNOPSIS>
+ <PARA>
+ Right clicking on the graph and selecting the
+ 'Configure...' option will display the 'Plot style' option for wiggle plots.
+ The plots can be displayed as histograms or as a heat map.
+ </PARA>
+ </LISTITEM>
+ <LISTITEM ID="GRAPH-FORMAT-4">
+ <PARA>
+ the last format supported by &prog; is fixedStep and is again a Wiggle format.
+ </PARA>
+<SYNOPSIS>
+track type=wiggle_0 name="fixedStep" description="fixedStep format" visibility=full autoScale=off viewLimits=0:1000 color=0,200,100 maxHeightPixels=100:50:20 graphType=points priority=20
+fixedStep chrom=chr19 start=7401 step=300 span=200
+1000
+ 900
+ 800
+ 700
+ 600
+ 500
+ 400
+ 300
+ 200
+ 100
+</SYNOPSIS>
+ </LISTITEM>
</ORDEREDLIST>
<PARA>