plotOneIdeo {trackViewer} | R Documentation

## plot ideogram with data for one chromosome

### Description

plot ideogram with data for one chromosome

### Usage

    plotOneIdeo(
      ideo,
      dataList,
      parameterList = list(vp = plotViewport(margins = c(0.1, 4.1, 1.1, 0.1)), ideoHeight =
        unit(1/(1 + length(dataList)), "npc"), vgap = unit(1, "lines"), ylabs =
        seqlevels(ideo)[1], ylabsRot = 90, ylabsPos = unit(2.5, "lines"), xaxis = FALSE,
        yaxis = FALSE, xlab = "", types = "barplot", heights = NULL, dataColumn = "score",
        gps = gpar(col = "black", fill = "gray")),
      chrom = seqlevels(ideo)[1],
      colorSheme = gieStain(),
      gp = gpar(fill = NA, lwd = 2),
      ...
    )

### Arguments

`ideo` | output of loadIdeogram.
`dataList` | a GRangesList of data to plot.
`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.
`chrom` | A length 1 character vector of chromosome name.
`colorSheme` | A character vector of giemsa stain colors.
`gp` | parameters used for grid.roundrect.
`...` | parameters not used.

### Examples

    ## Not run:
    ideo <- loadIdeogram("hg38")
    library(rtracklayer)
    library(grid)
    dataList <- ideo[seqnames(ideo) %in% "chr1"]
    dataList$score <- as.numeric(dataList$gieStain)
    dataList <- dataList[dataList$gieStain!="gneg"]
    dataList <- GRangesList(dataList, dataList)
    grid.newpage()
    plotOneIdeo(ideo, dataList, chrom="chr1")

    ## End(Not run)

[Package trackViewer version 1.24.2 Index]