plotProfile {GLAD} | R Documentation |
Plot genomic profile with breakpoints, outliers, smoothing line and cytogenetic banding.
plotProfile.profileCGH(profileCGH, variable="LogRatio", Chromosome=NULL, Smoothing=NULL, Bkp=FALSE, labels=TRUE, plotband=TRUE, unit=0, colDAGLAD=c("black","blue","red","green","yellow"), colCytoBand=c("white","darkblue"), colCentro="red", text=NULL, ...)
profileCGH |
Object of class profileCGH |
variable |
The variable to be plot. |
Chromosome |
A numeric vector with chromosome number to be
plotted. Use 23 and 24 for chromosome X and Y respectively. If
NULL , all the genome is plotted. |
Smoothing |
The variable used to plot the smoothing line. If
NULL , nothing is plotted. |
Bkp |
If TRUE , the breakpoints are represented by a
vertical red dashed line. |
labels |
If TRUE , the labels of the cytogenetic banding
are written. |
plotband |
If TRUE , the cytogenetic banding are plotted. |
unit |
Give the unit of the PosBase. For example if unit=3 ,
PosBase are in Kb, if unit=6 , PosBase are in Mb, ... |
colDAGLAD |
Color code to plot Deletion, Amplification, Gain, Lost and Normal status. |
colCytoBand |
Color code for cytogenetic banding. |
colCentro |
Color code for centromere. |
text |
A list with the parameters to be passed to the function text . |
... |
A plot
People interested in tools dealing with array CGH analysis can visit our web-page http://bioinfo.curie.fr.
Philippe Hupé, glad@curie.fr.
### Cytogenetic banding information data(cytoband) ### data(snijders) ### Creation of "profileCGH" object profileCGH <- as.profileCGH(gm13330) ########################################################### ### ### glad function as described in Hupé et al. (2004) ### ########################################################### res <- glad(profileCGH, mediancenter=FALSE, smoothfunc="lawsglad", bandwidth=10, round=2, model="Gaussian", lkern="Exponential", qlambda=0.999, base=FALSE, lambdabreak=8, lambdacluster=8, lambdaclusterGen=40, type="tricubic", param=c(d=6), alpha=0.001, msize=5, method="centroid", nmax=8, verbose=FALSE) ### Genomic profile on the whole genome plotProfile(res, unit=3, Bkp=TRUE, labels=FALSE, Smoothing="Smoothing", plotband=FALSE) ### Genomic profile on the whole genome and cytogenetic banding plotProfile(res, unit=3, Bkp=TRUE, labels=FALSE, Smoothing="Smoothing") ### Genomic profile for chromosome 1 text <- list(x=c(90000,200000),y=c(0.15,0.3),labels=c("NORMAL","GAIN"), cex=2) plotProfile(res, unit=3, Bkp=TRUE, labels=TRUE, Chromosome=1, Smoothing="Smoothing", plotband=FALSE, text=text) ### Genomic profile for chromosome 1 and cytogenetic banding with labels text <- list(x=c(90000,200000),y=c(0.15,0.3),labels=c("NORMAL","GAIN"), cex=2) plotProfile(res, unit=3, Bkp=TRUE, labels=TRUE, Chromosome=1, Smoothing="Smoothing", text=text, main="Chromosome 1")