annoSegments: Annotates a line segment within a plot

In PhanstielLab/BentoBox: Coordinate-Based Genomic Visualization Package for R

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()

PhanstielLab/BentoBox documentation built on June 30, 2024, 12:50 p.m.