annoSegments {plotgardener} | R Documentation

## Annotates a line segment within a plot

### Description

Annotates a line segment within a plot

### Usage

    annoSegments(
        x0,
        y0,
        x1,
        y1,
        plot,
        default.units = "native",
        linecolor = "black",
        lwd = 1,
        lty = 1,
        lineend = "butt",
        linejoin = "mitre",
        arrow = NULL,
        params = NULL,
        ...
    )

### Arguments

`x0` | A numeric vector or unit object indicating the starting x-values of the line segments.
`y0` | A numeric vector or unit object indicating the starting y-values of the line segments.
`x1` | A numeric vector or unit object indicating the stopping x-values of the line segments.
`y1` | A numeric vector or unit object indicating the stopping y-values of the line segments.
`plot` | Input plotgardener plot to internally plot line segments relative to.
`default.units` | A string indicating the default units to use if `x0`, `y0`, `x1`, or `y1` are only given as numeric vectors. Default value is `default.units = "native"`.
`linecolor` | A character value specifying segment line color. Default value is `linecolor = "black"`.
`lwd` | A numeric specifying segment line width. Default value is `lwd = 1`.
`lty` | A numeric specifying segment line type. Default value is `lty = 1`.
`lineend` | A character value specifying line end style. Default value is `lineend = "butt"`. Options are: `"round"`: Segment ends are rounded. `"butt"`: Segment ends end exactly where ended. `"square"`: Segment ends are squared.
`linejoin` | A character value specifying line join style. Default value is `linejoin = "mitre"`. Options are: `"round"`: Line joins are rounded. `"mitre"`: Line joins are sharp corners. `"bevel"`: Line joins are flattened corners.
`arrow` | A list describing arrow heads to place at either end of the line segments, as produced by the arrow function.
`params` | An optional pgParams object containing relevant function parameters.
`...` | Additional grid graphical parameters. See gpar.

### Value

Returns a `segments` object containing relevant placement and grob information.

### See Also

grid.segments, arrow

### Examples

    library(grid)
    ## Create a page
    pageCreate(width = 7.5, height = 2.5, default.units = "inches")

    ## Plot a Manhattan plot
    library(plotgardenerData)
    library("TxDb.Hsapiens.UCSC.hg19.knownGene")
    data("hg19_insulin_GWAS")
    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
    )

    ## Annotate a line segment for an additional significance line of
    ## the Manhattan plot
    annoSegments(
        x0 = unit(0, "npc"), y0 = 10,
        x1 = unit(1, "npc"), y1 = 10,
        plot = manhattanPlot, default.units = "native",
        linecolor = "red", lty = 2
    )

    ## 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"
    )

    ## Hide page guides
    pageGuideHide()

[Package plotgardener version 1.0.17 Index]