ideogramPlot {trackViewer} | R Documentation |
plot ideogram with data for multiple chromosomes
ideogramPlot(ideo, dataList, layout=NULL, horiz=TRUE, parameterList= list(vp=plotViewport(margins=c(.1, 4.1, .3, .1)), ideoHeight=unit(1/(1+length(dataList)), "npc"), vgap=unit(.3, "lines"), ylabs="auto", ylabsRot=ifelse(horiz, 0, 90), ylabsPos=unit(2.5, "lines"), xaxis=FALSE, yaxis=FALSE, xlab="", types="barplot", heights=NULL, dataColumn="score", gps=gpar(col="black", fill="gray")), colorSheme=gieStain(), gp=gpar(fill=NA, lwd=2), ...)
ideo |
output of loadIdeogram. |
dataList |
a GRangesList of data to plot. |
layout |
The layout of chromosomes. Could be a list with chromosome names as its elements. |
horiz |
a logical value. If FALSE, the ideograms are drawn vertically to the left. If TRUE, the ideograms are drawn horizontally at the bottom. |
parameterList |
parameterList a list of parameters for each dataset in the dataList. The elements of the parameters could be xlabs, ylabs, etc. type could be barplot, line, point, heatmap. |
colorSheme |
A character vector of giemsa stain colors. |
gp |
parameters used for grid.roundrect. |
... |
parameters not used. |
Jianhong Ou
See Also as loadIdeogram
## Not run: ideo <- loadIdeogram("hg38") library(rtracklayer) library(grid) dataList <- ideo dataList$score <- as.numeric(dataList$gieStain) dataList <- dataList[dataList$gieStain!="gneg"] dataList <- GRangesList(dataList) grid.newpage() ideogramPlot(ideo, dataList, layout=list("chr1", "chr2", c("chr3", "chr22"), c("chr4", "chr21"), c("chr5", "chr20"), c("chr6", "chr19"), c("chr7", "chr18"), c("chr8", "chr17"), c("chr9", "chr16"), c("chr10", "chr15"), c("chr11", "chr14"), c("chr12", "chr13"), c("chrX", "chrY")), parameterList = list(types="heatmap")) ## End(Not run)