plotPairs {plotgardener} | R Documentation

## Plot paired-end genomic range elements

### Description

Plot paired-end genomic range elements

### Usage

    plotPairs(
        data,
        chrom,
        chromstart = NULL,
        chromend = NULL,
        assembly = "hg38",
        fill = "#1f4297",
        linecolor = NA,
        bg = NA,
        boxHeight = unit(2, "mm"),
        spaceWidth = 0.02,
        spaceHeight = 0.3,
        limitLabel = TRUE,
        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"`.
`fill` | A single character value, a vector, or a colorby object specifying fill colors of paired range elements. Default value is `fill = "#1f4297"`.
`linecolor` | A single character value, a vector, or a colorby object specifying the color of the lines outlining paired range elements. Default value is `linecolor = NA`. Special options include: `NA`: No line color. `"fill"`: Same color as `fill`.
`bg` | Character value indicating background color. Default value is `bg = NA`.
`boxHeight` | A numeric or unit object specifying height of boxes at either end of paired range elements. Default value is `boxHeight = unit(2, "mm")`.
`spaceWidth` | A numeric specifying the width of spacing between paired range elements, as a fraction of the plot's genomic range. Default value is `spaceWidth = 0.02`.
`spaceHeight` | A numeric specifying the height of space between boxes of paired range elements on different rows. Default value is `spaceHeight = 0.3`.
`limitLabel` | A logical value indicating whether to draw a "+" when not all elements can be plotted in the plotting space. Default value is `limitLabel = TRUE`.
`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 paired range plot x-location.
`y` | A numeric, unit object, or character containing a "b" combined with a numeric value specifying paired range plot y-location. The character value will place the paired range 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 paired range plot width.
`height` | A numeric or unit object specifying paired range plot height.
`just` | Justification of paired range 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.
`params` | An optional pgParams object containing relevant function parameters.
`...` | Additional grid graphical parameters. See gpar.

### Details

#' A paired ranges plot can be placed on a plotgardener coordinate page by providing plot placement parameters:

    plotPairs(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 paired ranges plot by ignoring plot placement parameters:

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

### Value

Returns a `pairs` 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
    IMR90_DNAloops_pairs$length <-
            (IMR90_DNAloops_pairs$start2 - IMR90_DNAloops_pairs$start1) / 1000

    ## Plot the data
    bedpePlot <- plotPairs(
        data = IMR90_DNAloops_pairs, params = params,
        fill = colorby("length", palette =
                    colorRampPalette(c("dodgerblue2", "firebrick2"))),
        lwd = 2, spaceHeight = .7,
        x = 0.25, y = 0.25, height = 1.5,
        just = c("left", "top"), default.units = "inches"
    )

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

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

    ## Add heatmap legend label
    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]