annoZoomLines {plotgardener} | R Documentation

## Annotates zoom lines for a specified genomic region of a plot

### Description

Annotates zoom lines for a specified genomic region of a plot

### Usage

    annoZoomLines(
        plot,
        chrom,
        chromstart = NULL,
        chromend = NULL,
        y0,
        x1 = NULL,
        y1,
        extend = 0,
        default.units = "inches",
        linecolor = "grey",
        lty = 2,
        params = NULL,
        ...
    )

### Arguments

`plot` | Input plot to annotate genomic region zoom lines from.
`chrom` | Chromosome of region to draw zoom lines from, as a string.
`chromstart` | Integer start position on chromosome to draw zoom lines from.
`chromend` | Integer end position on chromosome to draw zoom lines from.
`y0` | A numeric vector or unit object indicating the starting y-values of the zoom line segments. If two values are given, the first value will correspond to the left zoom line and the second value will correspond to the right zoom line.
`x1` | A numeric vector or unit object indicating the stopping x-values of the zoom line segments. If two values are given, the first value will correspond to the left zoom line and the second value will correspond to the right zoom line. If NULL, straight lines from zoomed genomic region will be drawn.
`y1` | A numeric vector or unit object indicating the stopping y-values of the zoom line segments. If two values are given, the first value will correspond to the left zoom line and the second value will correspond to the right zoom line.
`extend` | A numeric vector or unit object indicating the length to extend straight lines from each end of the zoom line segments. If two values are given, the first value will correspond to the top extension length and the second value will correspond to the bottom extension length. Default value is `extend = 0`.
`default.units` | A string indicating the default units to use if `y0`, `x1`, `y1`, or `extend` are only given as numerics or numeric vectors. Default value is `default.units = "inches"`.
`linecolor` | A character value specifying zoom line color. Default value is `linecolor = "grey"`.
`lty` | A numeric specifying zoom line type. Default value is `lty = 2`.
`params` | An optional pgParams object containing relevant function parameters.
`...` | Additional grid graphical parameters. See gpar.

### Value

Returns a `zoom` object containing relevant genomic region, placement, and grob information.

### Examples

    ## Create a page
    pageCreate(width = 7.5, height = 4.75, default.units = "inches")

    ## Plot and place a Manhattan plot
    library(plotgardenerData)
    library("TxDb.Hsapiens.UCSC.hg19.knownGene")
    data("hg19_insulin_GWAS")
    manhattanPlot <- plotManhattan(
        data = hg19_insulin_GWAS, assembly = "hg19",
        fill = c("grey", "#37a7db"),
        sigLine = FALSE,
        col = "grey", lty = 2, range = c(0, 14),
        x = 0.5, y = 0, width = 6.5, height = 2,
        just = c("left", "top"),
        default.units = "inches"
    )
    annoYaxis(
        plot = manhattanPlot, at = c(0, 2, 4, 6, 8, 10, 12, 14),
        axisLine = TRUE, fontsize = 8
    )

    ## Annotate zoom lines for a region on chromsome 21
    zoomRegion <- pgParams(
        chrom = "chr21",
        chromstart = 28000000, chromend = 30300000,
        assembly = "hg19"
    )
    annoZoomLines(
        plot = manhattanPlot, params = zoomRegion,
        y0 = 2, x1 = c(0.5, 7), y1 = 2.5, extend = c(0, 1.1),
        default.units = "inches",
        lty = 3
    )

    ## Annotate highlight region for zoom region
    annoHighlight(
        plot = manhattanPlot, params = zoomRegion,
        y = 2, height = 2, just = c("left", "bottom"),
        default.units = "inches",
        fill = "red", alpha = 0.8
    )

    ## Plot Manhattan plot data and signal track under zoom lines
    manhattanPlotZoom <- plotManhattan(
        data = hg19_insulin_GWAS,
        fill = "grey",
        sigLine = FALSE,
        baseline = TRUE,
        params = zoomRegion, range = c(0, 14),
        x = 0.5, y = 2.6,
        width = 6.5, height = 1
    )
    data("IMR90_ChIP_H3K27ac_signal")
    signalPlot <- plotSignal(
        data = IMR90_ChIP_H3K27ac_signal, params = zoomRegion,
        range = c(0, 45),
        x = 0.5, y = "b0.1",
        width = 6.5, height = 0.65,
        just = c("left", "top"),
        default.units = "inches"
    )

    ## Plot genome label
    plotGenomeLabel(
        chrom = "chr21",
        chromstart = 28000000, chromend = 30300000,
        assembly = "hg19",
        x = 0.5, y = 4.4, length = 6.5,
        default.units = "inches"
    )

    ## Hide page guides
    pageGuideHide()

[Package plotgardener version 1.0.17 Index]