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(0.1, 4.1, 0.3, 0.1)), ideoHeight =
        unit(1/(1 + length(dataList)), "npc"), vgap = unit(0.3, "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` | 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.

### 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", colorKeyTitle="sample1"))

    ## End(Not run)

[Package trackViewer version 1.22.1 Index]