8
edits
Changes
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! scope="col" | Option
! scope="col" | Option
! scope="col" | Description
! scope="col" | Description
|-
|
|-
|-
| theme=
| theme=
| Select a theme. A theme is a collection of other settings. Options include theme=publication and theme=black.
| Select a theme. A theme is a collection of other settings. Options include theme=publication and theme=black.
|-
|-
| ymax
| ymax
| titleColor=black
| titleColor=black
| color for title
| color for title
| title=""
| title for plot
|-
| titleColor="black"
| color for title
|-
| width=10
| width of pdf (inches)
|-
| height=7
| height of pdf (inches)
|-
| leftMarginLines=5
| margin (in lines) on left
|-
| rightMarginLines=5
| margin (in lines) on right
|-
| unit=1000000
| bp per unit displayed in plot
|-
| showAnnot=TRUE
| show annotation for each snp?
|-
| showGenes=TRUE
| show genes?
|-
| annotCol='annotation'
| column to use for annotation, if it exists
|-
| annotPch='24,24,25,22,22,8,7,21,1'
| plot symbols for annotation
|-
| annotOrder=NULL
| ordering of annotation classes (comma-separated list annotation strings in order, alphabetical by default)
|-
| showRefsnpAnnot=TRUE
| show annotation for reference snp too?
|-
| bigDiamond=FALSE
| put big diamond around refsnp?
|-
| ld=NULL
| file for LD information
|-
| ldCuts="0,.2,.4,.6,.8,1"
| cut points for LD coloring
|-
| ldColors="gray50,navy,lightskyblue,green,orange,red,purple3"
| colors for LD
|-
| ldCol='rsquare'
| name for LD column
|-
| LDTitle=NULL
| title for LD legend
|-
| smallDot=.4
| smallest p-value cex
|-
| largeDot=.8
| largest p-value cex
|-
| refDot=NULL
| largest p-value cex
|-
| rfrows=4
| max number of rows used for displaying genes
|-
| showPartialGenes=TRUE
| should genes that don't fit completely be displayed?
|-
| geneFontSize=.8
| size for gene names
|-
| geneColor="navy"
| color for genes
|-
| snpsetFile=NULL
| use this file for SNPset data
|-
| rugColor=gray30
| color for snpset rugs
|-
| rugAlpha=1
| alpha for snpset rugs
|-
| metalRug=NULL
| if not null, use as label for rug of metal positions
|-
| showRecomb=TRUE
| show recombination rate?
|-
| recombColor=blue
| color for reccomb rate on plot
|-
| recombAxisColor=NULL
| color for reccomb rate axis labeing (default matches recombColor)
|-
| recombAxisAlpha=NULL
| color for reccomb rate axis labeing
|-
| recombOver=FALSE
| overlay recombination rate? (else underlay it)
|-
| recombFill=FALSE
| fill recombination rate? (else line only)
|-
| recombFillAlpha=0.2
| recomb fill alpha
|-
| recombLineAlpha=0.8
| recomb line/text alpha
|-
| frameColor=gray30
| frame color for plots
|-
| frameAlpha=1
| frame alpha for plots
|-
| legendSize=.8
| scaling factor of legend
|-
| legendAlpha=1
| transparency of legend background
|-
| legend='auto'
| legend? (auto, left, right, or none)
|-
| hiStart=0
| start of hilite region
|-
| hiEnd=0
| end of hilite region
|-
| hiColor=blue
| color used for hiliting
|-
| hiAlpha=0.1
| transparency level for highlighting
|-
| prelude=NULL
| R code to execute after data is read but before plot is made (allows data modification)
|-
| postlude=NULL,
| R code to execute after plot is made
|}
|}
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== Examples ==
== Examples ==
