IdiogramParams-class {VanillaICE} | R Documentation

## Paramater class for plotting idiograms

### Description

Paramater class for plotting idiograms

### Usage

    ## S4 method for signature 'IdiogramParams'
    show(object)

### Arguments

`object` | an IdiogramParam object

### Slots

`seqnames`

  length-one character vector providing chromosome name

`seqlengths`

  length-one numeric vector indicating size of chromosome

`unit`

  character string indicating unit for genomic position (default is 'kb')

`genome`

  character string indicating genome build

`box`

  a list of parameters for plotting the box around the part of the idiogram that is plotted.

### Examples

    if(require(BSgenome.Hsapiens.UCSC.hg18) && require(grid)){
       si <- seqinfo(BSgenome.Hsapiens.UCSC.hg18)
       iparam <- IdiogramParams(seqnames="chr1",
                                genome="hg18",
                                seqlengths=seqlengths(si)["chr1"],
                                box=list(xlim=c(20e6L, 25e6L), color="blue", lwd=2))
       iparam
       idiogram <- plot(iparam)
       vp <- viewport(x=0.05, y=0.8, width=unit(0.9, "npc"), height=unit(0.2, "npc"),
                      name="vp1", just=c("left", "bottom"))
       grid.newpage()
       pushViewport(vp)
       print(idiogram, vp=vp, newpage=FALSE)
    }

[Package VanillaICE version 1.42.4 Index]