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LocusZoom Standalone (view source)

Revision as of 09:38, 6 June 2010

158 bytes removed ,  09:38, 6 June 2010
→‎Plotting options
Line 364: Line 364:  
|-
 
|-
 
| axisSize=1
 
| axisSize=1
−
| sclaing factor for axes
+
| scaling factor for axes
 
|-
 
|-
 
| axisTextSize=1
 
| axisTextSize=1
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|-
 
|-
 
| refsnpTextSize=1
 
| refsnpTextSize=1
−
| sclaing factor for reference SNP text size
+
| scaling factor for reference SNP text size
 
|-
 
|-
 
| refsnpTextAlpha=1
 
| refsnpTextAlpha=1
 
| transparency level for reference SNP label (1=opaque,0=transparent)
 
| transparency level for reference SNP label (1=opaque,0=transparent)
−
|-
  −
| refsnpLineColor=transparent
  −
| color for ref snp line (invisible by default)
  −
|-
  −
| refsnpLineAlpha=.5
  −
| transparency level for reference snp line
   
|-
 
|-
 
| title = ""
 
| title = ""
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|-
 
|-
 
| annotCol='annotation'
 
| annotCol='annotation'
−
| column to use for annotation, if it exists
+
| column to use for custom annotation, if it exists
 
|-
 
|-
−
| annotPch='24,24,25,22,22, 8,7,21,1'   
+
| annotPch='24,24,25,22,22,8,7,21'   
 
| plot symbols for annotation
 
| plot symbols for annotation
 
|-
 
|-
 
| annotOrder=NULL
 
| annotOrder=NULL
−
| ordering of annotation classes (comma-separated list annotation strings in order, alphabetical by default)
+
| ordering of custom annotation classes (comma-separated list annotation strings in order, alphabetical by default)
 
|-
 
|-
 
| showRefsnpAnnot=TRUE
 
| showRefsnpAnnot=TRUE
 
| show annotation for reference snp too?
 
| show annotation for reference snp too?
−
|-
  −
| bigDiamond=FALSE
  −
| put big diamond around refsnp?
   
|-
 
|-
 
| ld=NULL
 
| ld=NULL
Line 466: Line 457:  
|-
 
|-
 
| snpsetFile=NULL
 
| snpsetFile=NULL
−
| use this file for SNPset data  
+
| use this file for SNPset rug data  
 
|-
 
|-
 
| rugColor=gray30
 
| rugColor=gray30
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|-
 
|-
 
| recombColor=blue
 
| recombColor=blue
−
| color for reccomb rate on plot
+
| color for recombination rate on plot
 
|-
 
|-
 
| recombAxisColor=NULL
 
| recombAxisColor=NULL
−
| color for reccomb rate axis labeing (default matches recombColor)
+
| color for recombination rate axis labeing (default matches recombColor)
 
|-
 
|-
 
| recombAxisAlpha=NULL
 
| recombAxisAlpha=NULL
−
| color for reccomb rate axis labeing
+
| color for recombination rate axis labeing
 
|-
 
|-
 
| recombOver=FALSE
 
| recombOver=FALSE
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|-
 
|-
 
| hiStart=0
 
| hiStart=0
−
| start of hilite region
+
| start of highlighted region
 
|-
 
|-
 
| hiEnd=0
 
| hiEnd=0
−
| end of hilite region
+
| end of highlighted region
 
|-
 
|-
 
| hiColor=blue
 
| hiColor=blue
−
| color used for hiliting
+
| color used for highlighting
 
|-
 
|-
 
| hiAlpha=0.1
 
| hiAlpha=0.1
Cristen
62

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Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/1635"

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