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]