plotGenes {plotgardener} | R Documentation

## Plot a gene track for a specified genomic region

### Description

Plot a gene track for a specified genomic region

### Usage

    plotGenes(
        chrom,
        chromstart = NULL,
        chromend = NULL,
        assembly = "hg38",
        fontsize = 8,
        fontcolor = c("#669fd9", "#abcc8e"),
        fill = c("#669fd9", "#abcc8e"),
        geneOrder = NULL,
        geneHighlights = NULL,
        geneBackground = "grey",
        strandLabels = TRUE,
        stroke = 0.1,
        bg = NA,
        x = NULL,
        y = NULL,
        width = NULL,
        height = unit(0.6, "inches"),
        just = c("left", "top"),
        default.units = "inches",
        draw = TRUE,
        params = NULL
    )

### Arguments

`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"`.
`fontsize` | A numeric specifying text fontsize in points. Default value is `fontsize = 8`.
`fontcolor` | A character value or vector of length 2 indicating the fontcolors for the plus strand and minus strand gene labels. The first value will color the plus strand gene labels and the second value will color the minus strand gene labels. Default value is `fontcolor = c("#669fd9", "#abcc8e")`.
`fill` | A character value or vector of length 2 indicating the strand fill colors for the plus strand and minus strand plot elements. The first value will color the plus strand plot elements and the second label will color the minus strand plot elements. Default value is `fill = c("#669fd9", "#abcc8e")`.
`geneOrder` | An ordered character vector of gene names to prioritize when labeling genes.
`geneHighlights` | A two-column dataframe with a column named "gene" containing gene names as strings to highlight and a named column "color" containing corresponding highlight colors.
`geneBackground` | If `geneHighlights` is given, a character value indicating the color for genes that are not highlighted.
`strandLabels` | A logical value indicating whether to include + and - strand labels to the left of the gene track.
`stroke` | A numeric value indicating the stroke width for gene body outlines. Default value is `stroke = 0.1`.
`bg` | Character value indicating background color. Default value is `bg = NA`.
`x` | A numeric or unit object specifying genes plot x-location.
`y` | A numeric, unit object, or character containing a "b" combined with a numeric value specifying genes plot y-location. The character value will place the genes 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 genes plot width.
`height` | A numeric or unit object specifying genes plot height.
`just` | Justification of genes 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.

### Details

A gene track can be placed on a page by providing plot placement parameters:

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

This function can be used to quickly plot an unnannotated gene track by ignoring plot placement parameters:

    plotGenes(chrom, chromstart = NULL, chromend = NULL)

Genomic annotation information is acquired through TxDb and OrgDb-class packages, as determined through the `assembly` parameter. To avoid overcrowding of gene name labels, plotted gene labels are by default prioritized according to citation counts.

### Value

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

### See Also

assembly, genomes, defaultPackages

### Examples

    ## Load hg19 genomic annotation packages
    library("TxDb.Hsapiens.UCSC.hg19.knownGene")
    library("org.Hs.eg.db")

    ## Set genomic coordinates
    paramssmall <- pgParams(
        chrom = "chr8",
        chromstart = 1, chromend = 3000000,
        assembly = "hg19", width = 7
    )
    paramsbig <- pgParams(
        chrom = "chr8",
        chromstart = 1, chromend = 146364022,
        assembly = "hg19", width = 7
    )
    ## Set colors
    cols <- c("#41B6C4", "#225EA8")

    ## Create page
    pageCreate(width = 7.5, height = 3.5, default.units = "inches")

    ## Plot genes big
    genesPlot <- plotGenes(
        params = paramsbig, fill = cols,
        fontcolor = cols,
        x = 0.25, y = 0.25, height = 0.75,
        just = c("left", "top"),
        default.units = "inches"
    )

    ## Annotate genome label
    annoGenomeLabel(
        plot = genesPlot, x = 0.25, y = 1.0,
        scale = "Mb", just = c("left", "top")
    )

    ## Plot genes small
    genesPlot <- plotGenes(
        params = paramssmall,
        geneHighlights = data.frame(
            "gene" = c("DLGAP2"),
            "color" = c("#225EA8")
        ),
        geneBackground = "grey",
        x = 0.25, y = 2.25, height = 0.75,
        just = c("left", "top"), default.units = "inches"
    )

    ## Annotate genome label
    annoGenomeLabel(
        plot = genesPlot, x = 0.25, y = 3.0, scale = "Mb",
        just = c("left", "top")
    )

    ## Hide page guides
    pageGuideHide()

[Package plotgardener version 1.0.17 Index]