annoHighlight {plotgardener} | R Documentation

## Annotates a highlight box around a specified genomic region of a plot

### Description

Annotates a highlight box around a specified genomic region of a plot

### Usage

    annoHighlight(
        plot,
        chrom,
        chromstart = NULL,
        chromend = NULL,
        fill = "grey",
        linecolor = NA,
        alpha = 0.4,
        y,
        height,
        just = c("left", "top"),
        default.units = "inches",
        params = NULL,
        ...
    )

### Arguments

`plot` | Input plot on which to annotate genomic region.
`chrom` | Chromosome of region to be highlighted, as a string.
`chromstart` | Integer start position on chromosome to be highlighted.
`chromend` | Integer end position on chromosome to be highlighted.
`fill` | A character value specifying highlight box fill color. Default value is `fill = "grey"`.
`linecolor` | A character value specifying highlight box line color. Default value is `linecolor = NA`.
`alpha` | Numeric value specifying color transparency. Default value is `alpha = 0.4`.
`y` | A numeric, unit object, or character containing a "b" combined with a numeric value specifying square highlight box y-location. The character value will place the highlight box y relative to the bottom of the most recently plotted plot according to the units of the `plotgardener` page.
`height` | A numeric or unit object specifying highlight box height.
`just` | Justification of highlight box relative to its (x, y) location. If there are two values, the first value specifies horizontal justification and the second value specifies vertical justification. Possible string values are: `"left"`, `"right"`, `"centre"`, `"center"`, `"bottom"`, and `"top"`. Default value is `just = c("left", "top")`.
`default.units` | A string indicating the default units to use if `y` or `height` are only given as numerics or numeric vectors. Default value is `default.units = "inches"`.
`params` | An optional pgParams object containing relevant function parameters.
`...` | Additional grid graphical parameters. See gpar.

### Value

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

### Examples

    ## Create a page
    pageCreate(width = 7.5, height = 1.5, default.units = "inches")

    ## Plot and place a signal plot
    library(plotgardenerData)
    data("IMR90_ChIP_H3K27ac_signal")
    region <- pgParams(
        chrom = "chr21",
        chromstart = 28000000, chromend = 30300000,
        assembly = "hg19",
        range = c(0, 45)
    )
    signalPlot <- plotSignal(
        data = IMR90_ChIP_H3K27ac_signal, params = region,
        x = 0.5, y = 0.25, width = 6.5, height = 0.65,
        just = c("left", "top"),
        default.units = "inches"
    )

    ## Highlight genomic region on signal plot
    annoHighlight(
        plot = signalPlot,
        chrom = "chr21",
        chromstart = 29000000, chromend = 29125000,
        y = 0.25, height = 1, just = c("left", "top"),
        default.units = "inches"
    )

    ## Plot text label
    plotText(
        label = "region of interest", fontsize = 8, fontcolor = "black",
        x = 3.5, y = 0.2, just = "bottom", default.units = "inches"
    )

    ## Plot genome label
    plotGenomeLabel(
        chrom = "chr21",
        chromstart = 28000000, chromend = 30300000,
        assembly = "hg19",
        x = 0.5, y = 1.3, length = 6.5, default.units = "inches"
    )

    ## Hide page guides
    pageGuideHide()

[Package plotgardener version 1.0.17 Index]