plotTranscripts {plotgardener} | R Documentation

## Plot gene transcripts in a pileup style for a single chromosome

### Description

Plot gene transcripts in a pileup style for a single chromosome

### Usage

    plotTranscripts(
        chrom,
        chromstart = NULL,
        chromend = NULL,
        assembly = "hg38",
        fill = c("#669fd9", "#abcc8e"),
        colorbyStrand = TRUE,
        strandSplit = FALSE,
        boxHeight = unit(2, "mm"),
        spaceWidth = 0.02,
        spaceHeight = 0.3,
        limitLabel = TRUE,
        fontsize = 8,
        labels = "transcript",
        stroke = 0.1,
        bg = NA,
        x = NULL,
        y = NULL,
        width = NULL,
        height = NULL,
        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"`.
`fill` | Character value(s) as a single value or vector specifying fill colors of transcripts. Default value is `fill = c("#669fd9", "#abcc8e")`.
`colorbyStrand` | A logical value indicating whether to color plus and minus strands by the first two colors in a `fill` vector, where plus strand transcripts will be colored by the first `fill` color and minus strand transcripts will be colored by the second `fill` color. Default value is `colorbyStrand = TRUE`.
`strandSplit` | A logical value indicating whether plus and minus-stranded transcripts should be separated, with plus strand transcripts plotted above the x-axis and minus strand transcripts plotted below the x-axis. Default value is `strandSplit = FALSE`.
`boxHeight` | A numeric or unit object specifying height of transcripts. Default value is `boxHeight = unit(2, "mm")`.
`spaceWidth` | A numeric value specifying the width of minimum spacing between transcripts, as a fraction of the plot's genomic range. Default value is `spaceWidth = 0.02`.
`spaceHeight` | A numeric value specifying the height of spacing between transcripts on different rows, as a fraction of `boxHeight`. 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`.
`fontsize` | A numeric specifying text fontsize in points. Default value is `fontsize = 8`.
`labels` | A character value describing the format of transcript text labels. Default value is `labels = "trancript"`. Options are: `NULL`: No labels. `"transcript"`: Transcript name labels. `"gene"`: Gene name labels. `"both"`: Combined transcript and gene name labels with the format "gene name:transcript name".
`stroke` | A numeric value indicating the stroke width for transcript 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 transcript plot x-location.
`y` | A numeric, unit object, or character containing a "b" combined with a numeric value specifying transcript plot y-location. The character value will place the transcript 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 transcript plot width.
`height` | A numeric or unit object specifying transcript plot height.
`just` | Justification of transcript 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 transcripts plot can be placed on a plotgardener coordinate page by providing plot placement parameters:

    plotTranscripts(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 transcripts plot by ignoring plot placement parameters:

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

Genomic annotation information is acquired through TxDb and OrgDb-class packages, as determined through the `assembly` parameter.

### Value

Returns a `transcripts` 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")

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

    ## Plot and place transcripts
    plotTranscripts(
        chrom = "chr8", chromstart = 1000000, chromend = 2000000,
        assembly = "hg19", labels = "gene",
        x = 0.5, y = 0.5, width = 6.5, height = 2.5,
        just = c("left", "top"), default.units = "inches"
    )

    ## Plot genome label
    plotGenomeLabel(
        chrom = "chr8", chromstart = 1000000, chromend = 2000000,
        assembly = "hg19",
        x = 0.5, y = 3.03, length = 6.5, default.units = "inches"
    )

    ## Plot a legend
    plotLegend(
        legend = c("+ strand", "- strand"),
        fill = c("#669fd9", "#abcc8e"), border = FALSE,
        x = 0.5, y = 1, width = 1, height = 0.5,
        just = c("left", "top")
    )

    ## Hide page guides
    pageGuideHide()

[Package plotgardener version 1.0.17 Index]