[Patchwork-commits] r193 - in pkg/patchwork: R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Sep 24 17:25:34 CEST 2013
Author: sebastian_d
Date: 2013-09-24 17:25:34 +0200 (Tue, 24 Sep 2013)
New Revision: 193
Added:
pkg/patchwork/R/patchwork.region.r
pkg/patchwork/R/sysdata.rda
pkg/patchwork/man/patchwork.region.Rd
Log:
added patchwork.region files to repository
Added: pkg/patchwork/R/patchwork.region.r
===================================================================
--- pkg/patchwork/R/patchwork.region.r (rev 0)
+++ pkg/patchwork/R/patchwork.region.r 2013-09-24 15:25:34 UTC (rev 193)
@@ -0,0 +1,578 @@
+#------------------------------------------------------------------------------------------------------
+#------------------------------------------------------------------------------------------------------
+#patchwork.region() ; a function for zooming in on a specific region and showing the regions genes.
+#------------------------------------------------------------------------------------------------------
+#------------------------------------------------------------------------------------------------------
+
+
+patchwork.region <- function(CNfile=NULL,chr,region,hg18=F)
+{
+ if (is.null(CNfile))
+ {
+ CNfile = list.files(pattern="*_copynumbers.Rdata")
+ if (length(CNfile)==0)
+ {
+ #cat("Could not find <sample>_copynumbers.Rdata in current working directory. Try again and supply patchwork.regions with the CNfile parameter.")
+ stop("Could not find <sample>_copynumbers.Rdata in current working directory. Try again and supply patchwork.regions with the CNfile parameter.")
+ }
+ if(length(CNfile)>1)
+ {
+ #cat("There seems to be more than one <sample>_copynumbers.Rdata file in the current working directory. Try again and supply patchwork.regions with the CNfile parameter.")
+ stop("There seems to be more than one <sample>_copynumbers.Rdata file in the current working directory. Try again and supply patchwork.regions with the CNfile parameter.")
+ }
+ }
+
+ #Load <sample>_copynumbers.Rdata giving us segs,alf and kbsegs
+ load(CNfile)
+
+ # #Set working directory and make that directorys name the samplename. If it is too long, shorten it.
+ # setwd(directory)
+ # subs <- getSubdirs()
+ # if (is.null(subs))
+ # { ## check samples = subdirectories or a single sample = current directory
+ # subs=thisSubdir()
+ # setwd('..')
+ # }
+
+ #store chr value in nchr because i made the newbie mistake of having a second variable also
+ #named chr.
+ nchr = chr
+
+ #get sample name
+ tmp_name <- strsplit(CNfile,split="_")
+ name=tmp_name[[1]][1]
+
+ #if sample name is too long, shorten it to 12 characters
+ if(nchar(name)>12)
+ {
+ name = substring(name,1,12)
+ }
+
+ #If nchr has been given as character
+ if(is.character(nchr) == T)
+ {
+ #If chr is longer than 2 characters ("chr1" but not "12")
+ #take out the number and convert it to numeric
+ if(nchar(nchr)>2)
+ {
+ c = strsplit(nchr,"chr")
+ c = as.numeric(c[[1]][2])
+ }
+ #chr has been given as character but without "chr" infront. Convert to numeric.
+ else
+ {
+ c = as.numeric(nchr)
+ }
+ }
+ #else chr has been given as a numeric and can be used directly.
+ else
+ {
+ c = nchr
+ }
+
+ #Rename parameters of <name>_copynumbers so we can re-use other plots as template.
+ chr = as.character(segs$chr)
+ start = segs$start
+ end = segs$end
+ int = segs$median
+ ai = segs$ai
+ mchr = as.character(kbsegs$chr)
+ mpos = kbsegs$pos
+ mval = kbsegs$ratio
+ schr = as.character(alf$achr)
+ spos = alf$apos
+ sval = (1-alf$amin/alf$amax)
+ xlim=c(0,2.5)
+ ylim=c(0,1)
+
+ #check if hg18 is true
+ #then load hg18 knownGene list
+ if(hg18==T)
+ {
+ kg = knownGene_hg18
+ }
+ else
+ {
+ kg = knownGene
+ }
+
+
+ #
+ #Here is where pretty normal plotting procedure starts
+ #
+
+ #Get ideogram #In sysdata.rda
+ #ideogram=getIdeogram()
+
+ #Set color gradient for p and q arm of chromosome
+ colors_p <- colorRampPalette(c("#6600FF","#9900CC"),space="rgb")
+ colors_q <- colorRampPalette(c("#CC0099","#CC0000"),space="rgb")
+
+ #filter the data (remove NA) and set some standard parameters
+ ai[is.na(ai)]=0
+ aix=ai!=0
+ chr=chr[aix]
+ start=start[aix]
+ end=end[aix]
+ int=int[aix]
+ ai=ai[aix]
+ pos <- (start+end)/2
+ length=end-start
+
+ size=rep(0.5,length(chr))
+ size[length>2000000]=1
+ size[length>5000000]=1.5
+ size[length>10000000]=2
+
+ #Select the chromosome
+ this <- ideogram[ideogram$c==c,]
+
+ #Extract regions start an stop
+ #region inputted in form start:stop
+ Rstart = min(region)
+ Rend = max(region)
+
+ #Initialize jpeg
+ jpeg(paste(name,'_',this$chr,'_region_',Rstart,"-",Rend,'.jpg',sep=''),width=11.7,height=8.3,units="in",res=300)
+
+ #split plot into desired formation
+ split.screen(as.matrix(data.frame(left=c(rep(0.05,4),rep(0.47,3)),
+ right=c(0.45,rep(1,6)),
+ bottom=c(0.50,0.05,0.2,0.3,0.50,0.70,0.75),
+ top = c(0.95,0.2,0.3,0.45,0.70,0.75,0.95)))) #screen 1-5
+
+
+ #Screen configuration overview
+ #-------------------------------------------------------------
+ #-------------------------------------------------------------
+ # | |
+ # | 7 |
+ # | |
+ # |------------------------------|
+ # 1 | 6 |
+ # |------------------------------|
+ # | |
+ # | 5 |
+ # | |
+ #-----------------------------|------------------------------|
+ # |
+ # 4 |
+ #------------------------------------------------------------|
+ # 3 |
+ #------------------------------------------------------------|
+ # |
+ # 2 |
+ #-------------------------------------------------------------
+
+
+ #------------------------------------------------------------
+ #Left side of the plot (Whole genome)
+ #------------------------------------------------------------
+
+ #index of overlapping the selected chromosome region to the chr object
+ wix <- chr==as.character(this$chr) & (((Rstart <= start) & (Rend >= end)) | ((Rstart >= start) & (Rstart <= end)) | ((Rend <= end) & (Rend >= start)))
+ ix <- chr==as.character(this$chr)
+
+ #Create an index of colors relating to the positions and lengths on this chromosome
+ col <- rep('#B0B0B030',length(chr))
+ col[wix & (pos < this$mid)] <- paste(colors_p(sum(wix & (pos < this$mid))), '70', sep='')
+ col[wix & (pos > this$mid)] <- paste(colors_q(sum(wix & (pos > this$mid))), '70', sep='')
+
+ #Go to screen 1
+ screen(1)
+
+ #Set marginals, outer marginals and mgp(which is for xlab,ylab,ticks and axis)
+ par(mar = c(0, 0, 0, 0))
+ par(oma = c(0,0,0,0))
+ par(mgp =c(0.5,0.25,0))
+
+ #Whole genome overview plot
+ #Note that we are plotting chrY in the background, despite the fact that it is not an "active" chromosome.
+ plot(c(int[!wix],int[wix]),c(ai[!wix],ai[wix]),
+ pch=16,
+ cex=c(size[!wix],size[wix]),
+ main = "",
+ xlab = "",
+ ylab = "",
+ axes=F, #Remove axis
+ col = c(col[!wix],col[wix]),
+ xlim = xlim,
+ ylim = ylim)
+
+ #Insert Y and X axis
+ axis(side=2,cex.axis=0.6,tck=0.963,col.ticks='#808080',at=seq(from=0,to=1,by=0.2),las=1)
+ axis(side=1,cex.axis=0.6,tck=0.963,col.ticks='#808080',at=seq(from=0,to=2.5,by=0.1))
+
+ #Titles,date/time and axis labels
+ mtext(text="Normalized coverage",side=1,line=1.1,cex=1)
+ mtext(text="Allelic imbalance",side=2,line=1.5,cex=1)
+ mtext(paste("Detailed view of sample: ",name,"\n Chromosome ",c,", Region: ",Rstart,"-",Rend,sep=""),side=3)
+
+ #------------------------------------------------------------
+ #Top Right - Signal
+ #------------------------------------------------------------
+
+ #Go to screen 7
+ screen(7)
+
+ #Set marginals, outer marginals and mgp(which is for xlab,ylab,ticks and axis)
+ par(mar = c(0, 0, 0, 0))
+ par(oma = c(0,0,0,0))
+ par(mgp =c(0.5,0,0))
+ par(xpd=T)
+
+ #Select the correct chromosome and remove stuff lower than -1
+ mix <- mchr==as.character(this$chr) #& mval>(-1)
+
+ #Create an index of colors relating to the positions and lengths on this chromosome
+ col=rep('#000000',sum(ix))
+ col[pos[ix] < this$mid] <- colors_p(sum(pos[ix] < this$mid))
+ col[pos[ix] > this$mid] <- colors_q(sum(pos[ix] > this$mid))
+
+ #Predefine ymin ymax and sequence between them
+ # ymin=floor(min(int[ix]))-0.5
+ # if(ymin > -1)
+ # {
+ # ymin = -1
+ # }
+ # ymax=ceiling(max(int[ix]))+0.5
+ # if(ymax < 1)
+ # {
+ # ymax = 1
+ # }
+ ymin=0
+ ymax=2.5
+ seqminmax=seq(ymin,ymax,by=0.5)
+
+ #Plot coverage over position
+ plot(mpos[mix],mval[mix],
+ pch=20,
+ cex=0.5,
+ main = "",
+ xlab = "",
+ ylab = "",
+ axes=F,
+ col = '#00000005',
+ xlim = c(0,this$length),
+ ylim = c(ymin,ymax))
+
+ #Add legend for red region
+ mtext(text=expression(bold("Selected region")),side=3,col='#E8000070',cex=0.8,adj=0.05)
+
+ #Add colored segments based on the log-ratio data
+ segments(x0=start[ix],x1=end[ix],
+ y0=int[ix],y1=int[ix],
+ col=col,
+ lwd=4)
+
+ #Add a rectangle showing which region has been chosen
+ rect(xleft=Rstart,xright=Rend,ybottom=ymin,ytop=ymax,col='#E8000040',lty=0)
+
+ #Add X and Y axis. The (side=4) axis is just a black line showing where the data ends
+ axis(side=2,tck=0.926,col.ticks='#808080',
+ #Set axis
+ #at=seq(from=-1,to=1.5,by=0.5),
+ #labels=c("-1","-.5","0",".5","1","1.5"),
+ #Dynamic axis
+ at=seqminmax,
+ #labels=paste(seqminmax,'',sep=''),
+ cex.axis=0.6,pos=0,hadj=1.3,las=1)
+
+ axis(side=4,labels=F,tck=0,pos=this$length,
+ at=seqminmax)
+
+ axis(side=1,tck=0.926,col.ticks='#808080',at=seq(5e6,this$length,by=5e6),
+ labels=FALSE,cex.axis=0.6,pos=ymin)
+
+ #Add Y axis label & date/time
+ mtext("Norm. coverage",side=2,line=0.3)
+ mtext(format(Sys.time(),"%Y-%m-%d %H:%M"),side=3,cex=0.6,adj=0.95)
+
+ #------------------------------------------------------------
+ #Middle Right - Cytobands
+ #------------------------------------------------------------
+
+ #Go to screen 6
+ screen(6)
+
+ #Set marginals, outer marginals and mgp(which is for xlab,ylab,ticks and axis)
+ par(mar = c(0, 0, 0, 0))
+ par(oma = c(0,0,0,0))
+ par(mgp =c(0.5,0,0))
+
+
+ #Create a empty plot with the same ylim and xlim as the plot directly above it (signal) and below (AI)
+ plot(0,0,xlab="",ylab="",main="",type="n",axes=F,xaxt="n",ylim=c(0,0.3),xlim=c(0,max(mpos[mix])))
+
+ #Add Y axis label
+ mtext(text="Cytoband",side=2,las=1,line=-1,cex=0.8)
+
+ #index of the chromData for this chromosome
+ dix = chromData$chr == as.character(this$chr)
+
+ #Add cytoband information as differently colored rectangles
+ rect(xleft=chromData$chromStart[dix],xright=chromData$chromEnd[dix],
+ #ybottom=0.15-chromData$thickness[dix]*0.03,ytop=0.15+chromData$thickness[dix]*0.03,
+ ybottom=0,ytop=0.3,
+ col=paste(chromData$col[dix],'99',sep=''),
+ lty=0)
+
+ #Add a rectangle showing which region has been chosen
+ rect(xleft=Rstart,xright=Rend,ybottom=0,ytop=0.3,col='#E8000040',lty=0)
+
+ #Att text annotation to cytobands
+ for(j in 1:length(chromData$name[dix]))
+ {
+ #If the cytoband region is larger than 5 Mb, it can fit some text
+ if((chromData$chromEnd[dix][j] - chromData$chromStart[dix][j]) > 4*10^6)
+ {
+ # Text is added at x position (all of previous chromosome) + (middle of region)
+ # The "srt" flips the text 90 degrees
+ text(x=(chromData$chromStart[dix][j]+((chromData$chromEnd[dix][j]-chromData$chromStart[dix][j])/2)),
+ y=0.15,labels=chromData$name[dix][j], srt=90,cex = 0.5,xpd=T)
+ }
+ }
+
+ #------------------------------------------------------------
+ #Bottom Right - Allelic imbalance
+ #------------------------------------------------------------
+
+ #Go to screen 5
+ screen(5)
+
+ #Set marginals, outer marginals and mgp(which is for xlab,ylab,ticks and axis)
+ par(mar = c(0, 0, 0, 0))
+ par(oma = c(0,0,0,0))
+ par(mgp =c(0.5,0,0))
+
+
+ #Index of correct chromsome and allele frequency not in either 0 or 1
+ six <- schr==as.character(this$chr) & !(sval %in% c(0,1))
+
+ #plot allele frequency over position
+ plot(spos[six],sval[six],
+ pch=20,
+ cex=0.5,
+ main = "",
+ xlab = "",
+ ylab = "",
+ #yaxt="n",
+ axes=F,
+ col = '#00000010',
+ xlim = c(0,this$length),
+ ylim = c(0,1))
+
+ #Add X and Y axis as well as a line to the rightmost of the data (side=4)
+ axis(side=2,tck=0.926,col.ticks='#808080',at=seq(from=0,to=1,by=0.2),cex.axis=0.6,pos=0,hadj=1.3,las=1)
+ axis(side=4,labels=F,tck=0,pos=this$length)
+ axis(side=1,tck=0.925,col.ticks='#808080',at=seq(5e6,this$length,by=5e6),
+ labels=paste(seq(5,round(this$length/1e6),5),'',sep=''),cex.axis=0.6,pos=0)
+
+ #Add a rectangle showing which region has been chosen
+ rect(xleft=Rstart,xright=Rend,ybottom=0,ytop=1,col='#E8000040',lty=0)
+
+ #Add X and Y label
+ mtext("Allelic imbalance",side=2,line=0.3)
+ mtext("Position (Mb)",side=1,line=1)
+
+ #------------------------------------------------------------
+ #Top Bottom - Detailed region coverage view
+ #------------------------------------------------------------
+
+ #Go to screen 4
+ screen(4)
+
+ #Set marginals, outer marginals and mgp(which is for xlab,ylab,ticks and axis)
+ par(mar = c(0, 0, 0, 0))
+ par(oma = c(0,0,0,0))
+ par(mgp =c(0.5,0,0))
+
+
+ #Select the correct chromosome and region and remove stuff lower than -1
+ mix <- mchr==as.character(this$chr) & (mpos >= Rstart) & (mpos <= Rend) #& mval>(-1)
+
+ wix <- chr==as.character(this$chr) & (((Rstart <= start) & (Rend >= end)) | ((Rstart >= start) & (Rstart <= end)) | ((Rend <= end) & (Rend >= start)))
+
+ cix = ((Rstart >= start) & (Rstart <= end))
+ start[cix] = Rstart
+ cix = ((Rend <= end) & (Rend >= start))
+ end[cix] = Rend
+
+ #Predefine ymin ymax and sequence between them
+ ymin=0
+ ymax=2.5
+ seqminmax=seq(ymin,ymax,by=0.5)
+
+ #Plot log-ratio over position
+ plot(mpos[mix],mval[mix],
+ pch=20,
+ cex=0.5,
+ main = "",
+ xlab = "",
+ ylab = "",
+ axes=F,
+ col = '#00000040',
+ xlim = c(Rstart,Rend),
+ ylim = c(ymin,ymax))#c(round(min(mval[mix]),digits=1),round(max(mval[mix]),digits=1)))#c(-1,1.5))
+
+ #Create an index of colors relating to the positions and lengths on this chromosome
+ col=rep('#000000',sum(wix))
+ col[pos[wix] < this$mid] <- colors_p(sum(pos[wix] < this$mid))
+ col[pos[wix] > this$mid] <- colors_q(sum(pos[wix] > this$mid))
+
+ #Add colored segments based on the log-ratio data
+ segments(x0=start[wix],x1=end[wix],
+ y0=int[wix],y1=int[wix],
+ col=col,
+ lwd=4)
+
+ #Add X and Y axis. The (side=4) axis is just a black line showing where the data ends
+ axis(side=2,tck=0.926,col.ticks='#808080',
+ #Set axis
+ #at=seq(from=-1,to=1.5,by=0.5),
+ #labels=c("-1","-.5","0",".5","1","1.5")
+ #Dynamic axis
+ at=seqminmax,
+ #labels=paste(seqminmax,'',sep=''),
+ ,cex.axis=0.6,pos=Rstart,hadj=1.3,las=1)
+
+ axis(side=4,labels=F,tck=0,pos=Rend)
+ #axis(side=1,tck=0.926,col.ticks='#808080',cex.axis=0.6,pos=-1)
+
+ #Add X Y axis label
+ mtext("Norm. coverage",side=2,line=-0.8)
+ #mtext("Position (Mb)",side=1,line=1)
+
+ #------------------------------------------------------------
+ #Middle Bottom - Region Gene view
+ #------------------------------------------------------------
+
+ #Go to screen 3
+ screen(3)
+
+ #Set marginals, outer marginals and mgp(which is for xlab,ylab,ticks and axis)
+ par(mar = c(0, 0, 0, 0))
+ par(oma = c(0,0,0,0))
+ par(mgp =c(0.5,0.25,0))
+
+ #par(xpd=T)
+
+ #Create a empty plot with the same ylim and xlim as the plot directly above it (signal) and below (AI)
+ plot(0,0,xlab="",ylab="",main="",type="n",axes=F,xaxt="n",ylim=c(0,0.48),xlim=c(Rstart,Rend))
+
+ kg=kg[order(kg$chr,kg$gtxEnd),]
+
+ #Create and index of the genes within region (rstart to rend)
+ #gix <- kg$chr==this$chr & (((Rstart <= kg$gtxStart) & (Rend >= kg$gtxEnd)) | ((Rstart >= kg$gtxStart) & (Rstart <= kg$gtxEnd)) | ((Rend <= kg$gtxEnd) & (Rend >= kg$gtxStart)))
+ gix <- kg$chr==as.character(this$chr) & ((Rstart <= kg$gtxEnd) & (Rend >= kg$gtxStart))
+
+ #If they are only partial overlapping, remove the parts outside of the selected region
+ cix = ((Rstart >= kg$gtxStart) & (Rstart <= kg$gtxEnd))
+ kg$gtxStart[cix] = Rstart
+ cix = ((Rend <= kg$gtxEnd) & (Rend >= kg$gtxStart))
+ kg$gtxEnd[cix] = Rend
+
+ # #Check if any genes are overlapping so they are shown on top of or below eachother
+ d1 = c(rep(0.42,length(which(gix))))
+ d2 = c(rep(0.36,length(which(gix))))
+ j = 1
+
+ for(i in min(which(gix)):max(which(gix)))
+ {
+ #if this gene overlaps with the gene infront of it
+ if(kg$gtxEnd[i] >= kg$gtxStart[i+1])
+ {
+ d1[j+1] = d1[j]-0.06
+ d2[j+1] = d2[j]-0.06
+ }
+ j = j + 1
+ }
+
+ #Add the genes to plot as horizontal rectangles that cover the transcribed region
+ rect(xleft=kg$gtxStart[gix],xright=kg$gtxEnd[gix],
+ #Between 0 - 0.3
+ ybottom=d2,ytop=d1,
+ col=rgb(kg$R[gix],kg$G[gix],kg$B[gix],maxColorValue=255),lty=1)
+
+ #Add legend
+ #
+ text(x=Rstart+(6.2*(Rend-Rstart)/10),y=0.46,labels=expression(bold("Feature in PDB")),col=rgb(0,0,0,maxColorValue=255),cex=0.6)
+ text(x=Rstart+(7.6*(Rend-Rstart)/10),y=0.46,labels=expression(bold("RefSeq,Swissprot or CCDS validated")),col=rgb(12,12,120,maxColorValue=255),cex=0.6)
+ text(x=Rstart+(9*(Rend-Rstart)/10),y=0.46,labels=expression(bold("Other RefSeq")),col=rgb(80,80,160,maxColorValue=255),cex=0.6)
+ text(x=Rstart+(9.8*(Rend-Rstart)/10),y=0.46,labels=expression(bold("non-RefSeq")),col=rgb(130,130,210,maxColorValue=255),cex=0.6)
+
+ #Add Y label
+ mtext("Known genes",side=2,line=-1.8,,cex=0.9,las=1)
+
+ #legend(c(Rstart,-1),legend=c("Black","Dark blue","Medium blue","Light blue"),cex=0.4,xpd=T,
+ # col=c(rgb(130,130,210,maxColorValue=255),
+ # rgb(12,12,120,maxColorValue=255),
+ # rgb(0,0,0,maxColorValue=255),
+ # rgb(80,80,160,maxColorValue=255)))
+
+ for(i in 1:length(kg$gAlias[gix]))
+ {
+ text(x=(kg$gtxStart[gix][i]+((kg$gtxEnd[gix][i]-kg$gtxStart[gix][i])/2)),
+ #This places the gAlias text at same hight level as the transcribed region rectangle.
+ #y=((d1[i]+d2[i])/2),
+ #This places the gAlias text at the bottom
+ y=0.08,
+ labels=kg$gAlias[gix][i],
+ #This makes the text vertical
+ srt=90,
+ cex = 0.4,xpd=T)
+ }
+
+
+
+ #------------------------------------------------------------
+ #Bottom Bottom - Detailed region allele frequency view
+ #------------------------------------------------------------
+
+ #Go to screen 2
+ screen(2)
+
+ #Set marginals, outer marginals and mgp(which is for xlab,ylab,ticks and axis)
+ par(mar = c(0, 0, 0, 0))
+ par(oma = c(0,0,0,0))
+ par(mgp =c(0.5,0.25,0))
+
+
+ #Index of correct chromsome and allele frequency not in either 0 or 1
+ six <- schr==as.character(this$chr) & !(sval %in% c(0,1)) & (spos >= Rstart) & (spos <= Rend)
+
+ #plot allele frequency over position
+ plot(spos[six],sval[six],
+ pch=20,
+ cex=0.5,
+ main = "",
+ xlab = "",
+ ylab = "",
+ #yaxt="n",
+ axes=F,
+ col = '#00000040',
+ xlim = c(Rstart,Rend),
+ ylim = c(0,1))
+
+ #Add X and Y axis as well as a line to the rightmost of the data (side=4)
+ axis(side=2,tck=0.926,col.ticks='#808080',at=seq(from=0,to=1,by=0.2),cex.axis=0.6,pos=Rstart,las=1)
+ axis(side=4,labels=F,tck=0,pos=Rend)
+ #axis(side=1,tck=0.925,col.ticks='#808080',at=seq(5e6,this$length,by=5e6),
+ # labels=paste(seq(5,round(this$length/1e6),5),'',sep=''),cex.axis=0.6,pos=0)
+ axis(side=1,cex.axis=0.6)
+
+ #Add X and Y label
+ mtext("Allelic imbalance",side=2,line=-0.8)
+ mtext("Position (Mb)",side=1,line=1)
+
+
+ #Close all the opened split.screens and release the figure
+ close.screen(all.screens=T)
+ dev.off()
+}
+
+
+
+
+
+
Added: pkg/patchwork/R/sysdata.rda
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Property changes on: pkg/patchwork/R/sysdata.rda
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Added: svn:mime-type
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Added: pkg/patchwork/man/patchwork.region.Rd
===================================================================
--- pkg/patchwork/man/patchwork.region.Rd (rev 0)
+++ pkg/patchwork/man/patchwork.region.Rd 2013-09-24 15:25:34 UTC (rev 193)
@@ -0,0 +1,115 @@
+\name{patchwork.region}
+\alias{Patchwork.Region}
+\alias{region}
+\alias{patchwork.region}
+
+
+\title{
+Detailed view of a selected regions of the genome.
+}
+
+\description{
+Visualises a selected regions on a selected chromosome for closer inspection. Also shows known genes for selected region.
+}
+
+\usage{
+patchwork.region(CNfile=NULL,chr,region,hg18=F)
+}
+
+\arguments{
+ \item{CNfile}{
+ The <sample>_copnumbers.Rdata file generated from patchwork.plot(). If kept at default, NULL, the current working directory will be searched for it.
+ }
+ \item{chr}{
+ Which chromosome you wish to view a region of. ex chr="1"
+ }
+ \item{region}{
+ The region in chromosomal coordinates you wish to view. ex region=1000000:6000000
+ }
+ \item{hg18}{
+ Gene list for hg19 aligned genome is default. Set hg18=T to use hg18 gene list.
+ }
+}
+
+\details{
+Walkthrough of the plot:
+
+\bold{TOP LEFT} \cr
+Vertical axis: Allelic imbalance \cr
+Horizontal axis: Normalized coverage \cr
+
+The selected regions segments in color, plotted agains the whole genome background in grey.
+
+\bold{TOP RIGHT - TOP} \cr
+Vertical axis: Normalized coverage \cr
+Horizontal axis: Position (Mb) \cr
+
+Normalized coverage of chromosome with selected region highlighted in a transparent red bar.
+
+\bold{TOP RIGHT - MIDDLE} \cr
+Horizontal axis: Position (Mb) \cr
+
+Cytoband information for chromosome with selected region highlighted in a transparent red bar.
+
+\bold{TOP RIGHT - BOTTOM} \cr
+Vertical axis: Allelic imbalance \cr
+Horizontal axis: Position (Mb) \cr
+
+Allelic imbalance of chromosome with selected region highlighted in a transparent red bar.
+
+\bold{BOTTOM - TOP} \cr
+Vertical axis: Normalized coverage \cr
+Horizontal axis: Position (Mb) \cr
+
+Normalized coverage of the selected region.
+
+\bold{BOTTOM - MIDDLE} \cr
+Horizontal axis: Position (Mb) \cr
+
+Known gene positions which are in the selected region.
+
+\bold{BOTTOM - BOTTOM} \cr
+Vertical axis: Allelic imbalance \cr
+Horizontal axis: Position (Mb) \cr
+
+Allelic imbalance of the selected region.
+
+}
+
+%\value{
+%% ~Describe the value returned
+%% If it is a LIST, use
+%% \item{comp1 }{Description of 'comp1'}
+%% \item{comp2 }{Description of 'comp2'}
+%% ...
+%}
+
+%\references{
+%% ~put references to the literature/web site here ~
+%}
+
+\author{
+Markus Mayrhofer, \email{markus.mayrhofer at medsci.uu.se}
+Sebastian DiLorenzo, \email{sebastian.dilorenzo at medsci.uu.se}
+}
+%\note{
+%% ~~further notes~~
+%}
+
+%% ~Make other sections like Warning with \section{Warning }{....} ~
+
+% \seealso{
+% \code{\link{patchwork.copynumbers}}
+% }
+
+%\examples{
+%##---- Should be DIRECTLY executable !! ----
+%##-- ==> Define data, use random,
+%##-- or do help(data=index) for the standard data sets.
+%Run examples of karyotype stuff. or not, maybe just point back to patchwork.plot.
+%}
+
+% Add one or more standard keywords, see file 'KEYWORDS' in the
+% R documentation directory.
+%\keyword{ ~kwd1 }
+%\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line
\ No newline at end of file
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