plotPairsArches {plotgardener} | R Documentation

## Plot paired-end genomic range data in an arch style

### Description

Plot paired-end genomic range data in an arch style

### Usage

    plotPairsArches(
        data,
        chrom,
        chromstart = NULL,
        chromend = NULL,
        assembly = "hg38",
        style = "2D",
        flip = FALSE,
        curvature = 5,
        archHeight = NULL,
        fill = "#1f4297",
        linecolor = NA,
        alpha = 0.4,
        bg = NA,
        clip = FALSE,
        clip.noAnchor = TRUE,
        range = NULL,
        baseline = FALSE,
        baseline.color = "grey",
        baseline.lwd = 1,
        x = NULL,
        y = NULL,
        width = NULL,
        height = NULL,
        just = c("left", "top"),
        default.units = "inches",
        draw = TRUE,
        params = NULL,
        ...
    )

### Arguments

`data` | A string specifying the BEDPE file path, a dataframe in BEDPE format specifying data to be plotted, or a GInteractions object.
`chrom` | Chromosome of region to be plotted, as a string.
`chromstart` | Integer start position on chromosome to be plotted.
`chromend` | Integer end position on chromosome to be plotted.
`assembly` | Default genome assembly as a string or a assembly object. Default value is `assembly = "hg38"`.
`style` | Character value describing the style of arches. Default value is `style = "2D"`. Options are: `"2D"`: Arches will be drawn in a 2-dimensional style. `"3D"`: Arches will be drawn in a 3-dimensional style.
`flip` | Logical value indicating whether to reflect arches over the x-axis. Default value is `flip = FALSE`.
`curvature` | Numeric indicating the number of points along the arch curvature. Default value is `curvature = 5`.
`archHeight` | Single numeric value, numeric vector, or column name in data specifying the arch heights. When NULL, all arches will be the same height, filling up the given plot area.
`fill` | A single character value, a vector, or a colorby object specifying fill colors of arches. Default value is `fill = #1f4297"`.
`linecolor` | A single character value, a vector, or a colorby object specifying the color of the lines outlining arches. Default value is `linecolor = NA`. Special options include: `NA`: No line color. `"fill"`: Same color as `fill`.
`alpha` | Numeric value specifying transparency. Default value is `alpha = 0.4`.
`bg` | Character value indicating background color. Default value is `bg = NA`.
`clip` | A logical value indicating whether to clip any arches that get cutoff in the given genomic region. Default value is `clip = FALSE`.
`clip.noAnchor` | A logical value indicating whether to clip any arches that overlap the given genomic region but do not have an anchor in that region. Default value is `clip.noAnchor = TRUE`.
`range` | A numeric vector of length 2 specifying the y-range of `archHeight` to plot (c(min, max)).
`baseline` | Logical value indicating whether to include a baseline along the x-axis. Default value is `baseline = FALSE`.
`baseline.color` | Baseline color. Default value is `baseline.color = "grey"`.
`baseline.lwd` | Baseline line width. Default value is `baseline.lwd = 1`.
`x` | A numeric or unit object specifying pair arches plot x-location.
`y` | A numeric, unit object, or character containing a "b" combined with a numeric value specifying BEDPE arches plot y-location. The character value will place the pair arches plot y relative to the bottom of the most recently plotted plot according to the units of the plotgardener page.
`width` | A numeric or unit object specifying pair arches plot width.
`height` | A numeric or unit object specifying pair arches plot height.
`just` | Justification of pair arches plot 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 `x`, `y`, `width`, or `height` are only given as numerics. Default value is `default.units = "inches"`.
`draw` | A logical value indicating whether graphics output should be produced. Default value is `draw = TRUE`.
`params` | An optional pgParams object containing relevant function parameters.
`...` | Additional grid graphical parameters. See gpar.

### Details

A pair arches plot can be placed on a plotgardener coordinate page by providing plot placement parameters:

    plotPairsArches(data chrom,
                    chromstart = NULL, chromend = NULL,
                    x, y, width, height, just = c("left", "top"),
                    default.units = "inches")

This function can also be used to quickly plot an unannotated pair arches plot by ignoring plot placement parameters:

    plotPairsArches(data, chrom,
                    chromstart = NULL, chromend = NULL)

### Value

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

### Examples

    ## Load paired ranges data in BEDPE format
    library(plotgardenerData)
    data("IMR90_DNAloops_pairs")

    ## Set the coordinates
    params <- pgParams(
        chrom = "chr21",
        chromstart = 27900000, chromend = 30700000,
        assembly = "hg19",
        width = 7
    )

    ## Create a page
    pageCreate(width = 7.5, height = 2.1, default.units = "inches")

    ## Add a length column to color by
    IMR90_DNAloops_pairs$length <-
            (IMR90_DNAloops_pairs$start2 - IMR90_DNAloops_pairs$start1) / 1000

    ## Translate lengths into heights
    IMR90_DNAloops_pairs$h <-
            IMR90_DNAloops_pairs$length / max(IMR90_DNAloops_pairs$length)

    ## Plot the data
    archPlot <- plotPairsArches(
        data = IMR90_DNAloops_pairs, params = params,
        fill = colorby("length", palette =
                    colorRampPalette(c("dodgerblue2", "firebrick2"))),
        linecolor = "fill",
        archHeight = "h", alpha = 1,
        x = 0.25, y = 0.25, height = 1.5,
        just = c("left", "top"),
        default.units = "inches"
    )

    ## Annotate genome label
    annoGenomeLabel(plot = archPlot, x = 0.25, y = 1.78, scale = "Mb")

    ## Annotate heatmap legend
    annoHeatmapLegend(
        plot = archPlot, fontcolor = "black",
        x = 7.0, y = 0.25,
        width = 0.10, height = 1, fontsize = 10
    )

    ## Add the heatmap legend title
    plotText(
        label = "Kb", rot = 90, x = 6.9, y = 0.75,
        just = c("center", "center"),
        fontsize = 10
    )

    ## Hide page guides
    pageGuideHide()

[Package plotgardener version 1.0.17 Index]