plotModelPeaks: Add expected peak locations

Description Usage Arguments Author(s) Examples

View source: R/plotModelPeaks.r

Description

Add expected peak locations to a plot obtained from showTumourProfile.

Usage

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plotModelPeaks(par = NULL, S = NULL, t = NULL, selectedPoints = NULL, 
               cn, epcol = "red", epcex = 3, eplwd = 3, eppch = 21, 
               spcol = "black", sppch = 19, spcex = 1, splwd = 1, 
               addlabels = F, preserveMatPatDiff=T, 
               preserveMaxSubClDiff=T , plot=TRUE , ...)

Arguments

par

$par values returned from a call of coverParamSpace (as in li[[1]]$par ). One of par or (S and t) must be given.

S

The S parameter.

t

The t parameter vector:

selectedPoints

Set of points selected with selectPeaks.

cn

Data frame of allowed copy-number configurations, typically created with prepCN from within coverParamSpace.

epcol

Color for expected peaks in epp.

epcex

Symbol expansion for expected peaks in epp.

eplwd

Line width for expected peaks in epp.

eppch

Plotting character for expected peaks in epp.

spcol

Color for selected peaks in selectedPoints.

sppch

Plotting character for selected peaks in selectedPoints.

spcex

Symbol expansion for selected peaks in selectedPoints.

splwd

Line width for selected peaks in selectedPoints.

addlabels

Flag to indicate that a call to addLabels is requested.

preserveMatPatDiff

Flag to indicate if the sign of the difference between (say) the paternal and maternal chromosome copy-number is to be consistent in each clones.

preserveMaxSubClDiff

maxsubcldiff is a parameter of prepCN that indicates the upper bound for the difference in copy number between any two subclones (when >=1). However, each parental chromosomes can have copy number differences greater than maxsubcldiff. This flag is used to indicate that maxsubcldiff is to be applied to each parental chromosomes.

plot

If FALSE, no points are plotted

...

Additional parameters passed to addLabels.

Author(s)

Mathieu Lemire

Examples

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## Not run: 
showTumourProfile(copyAr, maxPoints=50000 , flatten=.25 , nlev=20, 
       seed=12345  , xlim=c(0,2) , nx=200, ny=50  )
prepCN(12)
ePP<-plotModelPeaks( S= 0.6260699, t=c(0.02222, 0.97778),
       selectedPoints=sp,cn=cn, epcol="red",epcex=1,eplwd=3 )
addLabels( ePP, manual=T)

## End(Not run)

mathieu-lemire/celluloid_0.11 documentation built on May 31, 2018, 7:22 p.m.