annoHeatmapLegend: Add a color scale legend for heatmap-style plots

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

Add a color scale legend for heatmap-style plots

Description

Add a color scale legend for heatmap-style plots

Usage

annoHeatmapLegend(
    plot,
    orientation = "v",
    fontsize = 8,
    fontcolor = "dark grey",
    scientific = FALSE,
    digits = 1,
    ticks = FALSE,
    breaks = NULL,
    border = FALSE,
    x,
    y,
    width,
    height,
    just = c("left", "top"),
    default.units = "inches",
    params = NULL,
    ...
)

Arguments

plot	Heatmap-style plot object to add heatmap legend for.
orientation	A string specifying legend orientation. Default value is orientation = "v". Options are: "v": Vertical legend orientation. "h": Horizontal legend orientation.
fontsize	A numeric specifying text fontsize in points. Default value is fontsize = 8.
fontcolor	Character value specfying text fontcolor. Default value is fontcolor = "dark grey".
scientific	Logical value specifying if numeric color value labels should be encoded in scientific format. Default value is scientific = FALSE.
digits	Numeric specifying how many significant digits to include of numeric color value labels. Default value is digits = 1.
ticks	Logical value specifying if tick marks on the heatmap colorbar should be visible. Default value is ticks = FALSE.
breaks	A numeric vector specifying tick breaks. Default value is breaks = NULL.
border	Logical value indicating whether to add a border around heatmap legend. Default value is border = FALSE.
x	A numeric or unit object specifying x-location of legend.
y	A numeric, unit object, or character containing a "b" combined with a numeric value specifying y-location of legend. The character value will place the legend 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 width of legend.
height	A numeric or unit object specifying height of legend.
just	Justification of heatmap legend 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".
params	An optional pgParams object containing relevant function parameters.
...	Additional grid graphical parameters. See gpar.

Value

Returns a heatmapLegend object with relevant color value, placement, and grob information.

Examples

## Load Hi-C data
library(plotgardenerData)
data("IMR90_HiC_10kb")

## Create page
pageCreate(width = 4, height = 3.5, default.units = "inches")

## Plot and place a square Hi-C plot
hicPlot <- plotHicSquare(
    data = IMR90_HiC_10kb, resolution = 10000,
    zrange = c(0, 70),
    chrom = "chr21",
    chromstart = 28000000, chromend = 30300000,
    assembly = "hg19",
    x = 0.5, y = 0.5, width = 2.5, height = 2.5,
    just = c("left", "top"),
    default.units = "inches"
)

## Add heatmap legend
annoHeatmapLegend(
    plot = hicPlot,
    x = 3.2, y = 0.5, width = 0.12, height = 1.2,
    just = c("left", "top"), default.units = "inches"
)

## Annotate genome label
annoGenomeLabel(
    plot = hicPlot, x = 0.5, y = 3.03, scale = "Mb",
    just = c("left", "top")
)

## Hide page guides
pageGuideHide()

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