annoHighlight: Annotates a highlight box around a specified genomic region...

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

Annotates a highlight box around a specified genomic region of a plot

Description

Annotates a highlight box around a specified genomic region of a plot

Usage

annoHighlight(
    plot,
    chrom,
    chromstart = NULL,
    chromend = NULL,
    fill = "grey",
    linecolor = NA,
    alpha = 0.4,
    y,
    height,
    just = c("left", "top"),
    default.units = "inches",
    params = NULL,
    ...
)

Arguments

plot	Input plot on which to annotate genomic region.
chrom	Chromosome of region to be highlighted, as a string.
chromstart	Integer start position on chromosome to be highlighted.
chromend	Integer end position on chromosome to be highlighted.
fill	A character value specifying highlight box fill color. Default value is fill = "grey".
linecolor	A character value specifying highlight box line color. Default value is linecolor = NA.
alpha	Numeric value specifying color transparency. Default value is alpha = 0.4.
y	A numeric, unit object, or character containing a "b" combined with a numeric value specifying square highlight box y-location. The character value will place the highlight box y relative to the bottom of the most recently plotted plot according to the units of the plotgardener page.
height	A numeric or unit object specifying highlight box height.
just	Justification of highlight box 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 y or height are only given as numerics or numeric vectors. Default value is default.units = "inches".
params	An optional pgParams object containing relevant function parameters.
...	Additional grid graphical parameters. See gpar.

Value

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

Examples

## Create a page
pageCreate(width = 7.5, height = 1.5, default.units = "inches")

## Plot and place a signal plot
library(plotgardenerData)
data("IMR90_ChIP_H3K27ac_signal")
region <- pgParams(
    chrom = "chr21",
    chromstart = 28000000, chromend = 30300000,
    assembly = "hg19",
    range = c(0, 45)
)
signalPlot <- plotSignal(
    data = IMR90_ChIP_H3K27ac_signal, params = region,
    x = 0.5, y = 0.25, width = 6.5, height = 0.65,
    just = c("left", "top"),
    default.units = "inches"
)

## Highlight genomic region on signal plot
annoHighlight(
    plot = signalPlot,
    chrom = "chr21",
    chromstart = 29000000, chromend = 29125000,
    y = 0.25, height = 1, just = c("left", "top"),
    default.units = "inches"
)

## Plot text label
plotText(
    label = "region of interest", fontsize = 8, fontcolor = "black",
    x = 3.5, y = 0.2, just = "bottom", default.units = "inches"
)

## Plot genome label
plotGenomeLabel(
    chrom = "chr21",
    chromstart = 28000000, chromend = 30300000,
    assembly = "hg19",
    x = 0.5, y = 1.3, length = 6.5, default.units = "inches"
)

## Hide page guides
pageGuideHide()

PhanstielLab/plotgardener documentation built on July 1, 2024, 7:06 p.m.