ideogramPlot {trackViewer}R Documentation

plot ideogram with data

Description

plot ideogram with data for multiple chromosomes

Usage

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), ...)

Arguments

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.

Author(s)

Jianhong Ou

See Also

See Also as loadIdeogram

Examples

## 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)

[Package trackViewer version 1.14.1 Index]