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Commit 99e74805 authored by tjc's avatar tjc
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add docs on wiggle plots

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@11374 ee4ac58c-ac51-4696-9907-e4b3aa274f04
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...@@ -1545,7 +1545,7 @@ GUG 8.3( 12422) GCG 5.3( 8011) GAG 21.3( 31979) GGG 4.3( 6497) ...@@ -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 &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 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 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> </PARA>
<ORDEREDLIST ID="GRAPH-FORMAT"> <ORDEREDLIST ID="GRAPH-FORMAT">
...@@ -1572,11 +1572,14 @@ of two possible graph file formats: ...@@ -1572,11 +1572,14 @@ of two possible graph file formats:
<PARA> <PARA>
the first column corresponds to the base position and is an integer. the first column corresponds to the base position and is an integer.
Note to distinguish this format from the previous format the first 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: values. Example extract:
<SYNOPSIS> <SYNOPSIS>
# BASE VAL1 VAL2 VAL3 VAL4 VAL5 VAL6 # 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 0 536.04 176 2204.8 848.23 0 0 0 536.04
278 804.99 0 837.2 0 681.63 0 278 804.99 0 837.2 0 681.63 0
452 0 699.98 0 0 0 251.18 452 0 699.98 0 0 0 251.18
...@@ -1589,6 +1592,49 @@ of two possible graph file formats: ...@@ -1589,6 +1592,49 @@ of two possible graph file formats:
</PARA> </PARA>
</LISTITEM> </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> </ORDEREDLIST>
<PARA> <PARA>
......
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