plotHicTriangle {plotgardener} | R Documentation

## Plot a Hi-C interaction matrix in a triangular format

### Description

Plot a Hi-C interaction matrix in a triangular format

### Usage

    plotHicTriangle(
        data,
        resolution = "auto",
        zrange = NULL,
        norm = "KR",
        matrix = "observed",
        chrom,
        chromstart = NULL,
        chromend = NULL,
        assembly = "hg38",
        palette = colorRampPalette(brewer.pal(n = 9, "YlGnBu")),
        colorTrans = "linear",
        flip = FALSE,
        bg = NA,
        x = NULL,
        y = NULL,
        width = NULL,
        height = NULL,
        just = c("left", "top"),
        default.units = "inches",
        draw = TRUE,
        params = NULL,
        quiet = FALSE
    )

### Arguments

`data` | Path to .hic file as a string or a 3-column dataframe of interaction counts in sparse upper triangular format.
`resolution` | A numeric specifying the width in basepairs of each pixel. For hic files, "auto" will attempt to choose a resolution based on the size of the region. For dataframes, "auto" will attempt to detect the resolution the dataframe contains.
`zrange` | A numeric vector of length 2 specifying the range of interaction scores to plot, where extreme values will be set to the max or min.
`norm` | Character value specifying hic data normalization method, if giving .hic file. This value must be found in the .hic file. Default value is `norm = "KR"`.
`matrix` | Character value indicating the type of matrix to output. Default value is `matrix = "observed"`. Options are: `"observed"`: Observed counts. `"oe"`: Observed/expected counts. `"log2oe"`: Log2 transformed observed/expected counts.
`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"`.
`palette` | A function describing the color palette to use for representing scale of interaction scores. Default value is `palette = colorRampPalette(brewer.pal(n = 9, "YlGnBu"))`.
`colorTrans` | A string specifying how to scale Hi-C colors. Options are "linear", "log", "log2", or "log10". Default value is `colorTrans = "linear"`.
`flip` | A logical indicating whether to flip the orientation of the Hi-C matrix over the x-axis. Default value is `flip = FALSE`.
`bg` | Character value indicating background color. Default value is `bg = NA`.
`x` | A numeric or unit object specifying triangle Hi-C plot x-location.
`y` | A numeric, unit object, or character containing a "b" combined with a numeric value specifying triangle Hi-C plot y-location. The character value will place the triangle Hi-C 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 the bottom width of the Hi-C plot triangle.
`height` | A numeric or unit object specifying the height of the Hi-C plot triangle.
`just` | Justification of triangle Hi-C 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.
`quiet` | A logical indicating whether or not to print messages.

### Details

A triangle Hi-C plot can be placed on a plotgardener coordinate page by providing plot placement parameters:

    plotHicTriangle(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 triangle Hi-C plot by ignoring plot placement parameters:

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

If `height` is < 0.5 * width, the top of the triangle will be cropped to the given `height`.

### Value

Returns a `hicTriangle` object containing relevant genomic region, Hi-C data, placement, and grob information.

### See Also

readHic

### Examples

    ## Load Hi-C data
    library(plotgardenerData)
    data("IMR90_HiC_10kb")

    ## Create a page
    pageCreate(width = 4, height = 2.5, default.units = "inches")

    ## Plot and place triangle Hi-C plot
    hicPlot <- plotHicTriangle(
        data = IMR90_HiC_10kb, resolution = 10000,
        zrange = c(0, 70),
        chrom = "chr21",
        chromstart = 28000000, chromend = 30300000,
        assembly = "hg19", bg = "black",
        x = 2, y = 0.5, width = 3, height = 1.5,
        just = "top", default.units = "inches"
    )

    ## Annotate x-axis genome label
    annoGenomeLabel(
        plot = hicPlot, scale = "Mb", x = 0.5, y = 2.03,
        just = c("left", "top")
    )

    ## Annotate heatmap legend
    annoHeatmapLegend(
        plot = hicPlot, x = 3.5, y = 0.5,
        width = 0.13, height = 1.2,
        just = c("right", "top")
    )

    ## Hide page guides
    pageGuideHide()

[Package plotgardener version 1.0.17 Index]