plotManhattan {plotgardener} | R Documentation

## Plot a Manhattan plot

### Description

Plot a Manhattan plot

### Usage

    plotManhattan(
        data,
        sigVal = 5e-08,
        chrom = NULL,
        chromstart = NULL,
        chromend = NULL,
        assembly = "hg38",
        fill = "black",
        pch = 19,
        cex = 0.25,
        leadSNP = NULL,
        sigLine = FALSE,
        sigCol = NULL,
        range = NULL,
        space = 0.01,
        bg = NA,
        baseline = FALSE,
        baseline.color = "grey",
        baseline.lwd = 1,
        x = NULL,
        y = NULL,
        width = NULL,
        height = NULL,
        just = c("left", "top"),
        flip = FALSE,
        default.units = "inches",
        draw = TRUE,
        params = NULL,
        ...
    )

### Arguments

`data` | Data to be plotted, as a character value specifying a file path of GWAS data, a dataframe, or a GRanges object. Each of these data types must have the following columns: `"chrom"`: Chromosome names. This column must be a character. `"pos"`: Chromosomal position. This column must be an integer or numeric. `"p"`: p-value. This column must be numeric. p-values will be converted to -log(10) space. `"snp"`(optional): SNP name or rsid. This column should be a character.
`sigVal` | A numeric specifying the significance level of p-values. Along with data p-values, this value will be converted to -log(10) space. Default value is `sigVal = 5e-08`.
`chrom` | Chromosome of region to be plotted, as a string. If left `NULL`, all chromosomes found in data will be plotted.
`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 data points. For a Manhattan plot with multiple chromosomes, a vector of colors will be used to color points of different chromosomes. Default value is `fill = "black"`.
`pch` | A numeric value or numeric vector specifying point symbols. If colorby object is supplied for `fill`, point symbols will be mapped to `colorby` values. Default value is `pch = 19`.
`cex` | A numeric indicating the amount by which points should be scaled relative to the default. Default value is `cex = 0.25`.
`leadSNP` | A list specifying the lead SNP in the desired region and any associated aesthetic features of the lead SNP data point and text label. The lead SNP should be specified as a character with the name slot `"snp"` in the list. Accepted lead SNP aesthetic features in the list include `fill`, `pch`, `cex`, `fontcolor`, and `fontsize`.
`sigLine` | Logical value indicating whether to draw a line at the significance level indicated with `sigVal`. Default value is `sigLine = FALSE`.
`sigCol` | Single character value specifying the color of significant data points.
`range` | A numeric vector of length 2 specifying the y-range of p-values to plot (c(min, max)).
`space` | A numeric value indicating the space between each chromosome as a fraction of the width of the plot, if plotting multiple chromosomes. Default value is `space = 0.01`.
`bg` | Character value indicating background color. Default value is `bg = NA`.
`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 Manhattan plot x-location.
`y` | A numeric, unit object, or character containing a "b" combined with a numeric value specifying Manhattan plot y-location. The character value will place the Manhattan 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 Manhattan plot width.
`height` | A numeric or unit object specifying Manhattan plot height.
`just` | Justification of Manhattan 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")`.
`flip` | Logical value indicating whether to reflect Manhattan plot over the x-axis. Default value is `flip = FALSE`.
`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 Manhattan plot can be placed on a plotgardener coordinate page by providing plot placement parameters:

    plotManhattan(data,
                    chrom = NULL,
                    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 Manhattan plot by ignoring plot placement parameters:

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

### Value

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

### Examples

    ## Load genomic assembly information
    library("TxDb.Hsapiens.UCSC.hg19.knownGene")
    ## Load GWAS data
    library(plotgardenerData)
    data("hg19_insulin_GWAS")

    ## Create a page
    pageCreate(width = 7.5, height = 4.5, default.units = "inches")

    ## Plot all GWAS data
    manhattanPlot <- plotManhattan(
        data = hg19_insulin_GWAS, assembly = "hg19",
        fill = c("grey", "#37a7db"),
        sigLine = TRUE,
        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"
    )
    ## Annotate genome label
    annoGenomeLabel(
        plot = manhattanPlot, x = 0.5, y = 2, fontsize = 8,
        just = c("left", "top"),
        default.units = "inches"
    )
    plotText(
        label = "Chromosome", fontsize = 8,
        x = 3.75, y = 2.20, just = "center", default.units = "inches"
    )

    ## Annotate y-axis
    annoYaxis(
        plot = manhattanPlot, at = c(0, 2, 4, 6, 8, 10, 12, 14),
        axisLine = TRUE, fontsize = 8
    )

    ## Plot y-axis label
    plotText(
        label = "-log10(p-value)", x = 0.15, y = 1, rot = 90,
        fontsize = 8, fontface = "bold", just = "center",
        default.units = "inches"
    )

    ## Plot GWAS data zooming in on chromosome 11
    ## highlighting a lead SNP, and coloring by LD score
    hg19_insulin_GWAS$LD <- as.numeric(hg19_insulin_GWAS$LD)
    ## Group LD column into LD ranges
    hg19_insulin_GWAS <- as.data.frame(dplyr::group_by(hg19_insulin_GWAS,
                                            LDgrp = cut(
                                            hg19_insulin_GWAS$LD,
                                            c(0, 0.2, 0.4, 0.6, 0.8, 1))))
    hg19_insulin_GWAS$LDgrp <- addNA(hg19_insulin_GWAS$LDgrp)
    leadSNP_p <- min(hg19_insulin_GWAS[
        which(hg19_insulin_GWAS$chrom == "chr11"), ]$p)
    leadSNP <- hg19_insulin_GWAS[which(hg19_insulin_GWAS$p == leadSNP_p), ]$snp
    chr11_manhattanPlot <- plotManhattan(
        data = hg19_insulin_GWAS, chrom = "chr11",
        chromstart = 60000000,
        chromend = 130000000,
        assembly = "hg19",
        fill = colorby("LDgrp",
        palette = colorRampPalette(c(
            "#1f4297",
            "#37a7db", "green",
            "orange", "red", "grey"
        ))),
        sigLine = TRUE, col = "grey",
        lty = 2, range = c(0, 16),
        leadSNP = list(
            snp = leadSNP,
            pch = 18,
            cex = 0.75,
            fill = "#7ecdbb",
            fontsize = 8
        ),
        x = 0.5, y = 2.5, width = 6.5,
        height = 1.5,
        just = c("left", "top"),
        default.units = "inches"
    )

    ## Plot legend for LD scores
    plotLegend(
        legend = c(
            "LD Ref Var",
            paste("0.4", ">", "r^2",
            "", ">=", "0.2"),
            paste("0.2", ">", "r^2",
            "", ">=", "0"),
            "no LD data"
        ),
        fill = c("#7ecdbb", "#37a7db", "#1f4297", "grey"), cex = 0.75,
        pch = c(18, 19, 19, 19), border = FALSE, x = 7, y = 2.5,
        width = 1.5, height = 0.6, just = c("right", "top"),
        default.units = "inches"
    )

    ## Annotate genome label
    annoGenomeLabel(
        plot = chr11_manhattanPlot, x = 0.5, y = 4.01,
        fontsize = 8, scale = "Mb",
        just = c("left", "top"), default.units = "inches"
    )

    ## Annotate y-axis
    annoYaxis(
        plot = chr11_manhattanPlot,
        at = c(0, 2, 4, 6, 8, 10, 12, 14, 16),
        axisLine = TRUE, fontsize = 8
    )

    ## Plot y-axis label
    plotText(
        label = "-log10(p-value)", x = 0.15, y = 3.25, rot = 90,
        fontsize = 8, fontface = "bold", just = "center",
        default.units = "inches"
    )

    ## Hide page guides
    pageGuideHide()

[Package plotgardener version 1.0.17 Index]