plotGenes: Plot a gene track for a specified genomic region

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

Plot a gene track for a specified genomic region

Description

Plot a gene track for a specified genomic region

Usage

plotGenes(
    chrom,
    chromstart = NULL,
    chromend = NULL,
    assembly = "hg38",
    fontsize = 8,
    fontcolor = c("#669fd9", "#abcc8e"),
    fill = c("#669fd9", "#abcc8e"),
    geneOrder = NULL,
    geneHighlights = NULL,
    geneBackground = "grey",
    strandLabels = TRUE,
    stroke = 0.1,
    bg = NA,
    x = NULL,
    y = NULL,
    width = NULL,
    height = unit(0.6, "inches"),
    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".
fontsize	A numeric specifying text fontsize in points. Default value is fontsize = 8.
fontcolor	A character value or vector of length 2 indicating the fontcolors for the plus strand and minus strand gene labels. The first value will color the plus strand gene labels and the second value will color the minus strand gene labels. Default value is fontcolor = c("#669fd9", "#abcc8e").
fill	A character value or vector of length 2 indicating the strand fill colors for the plus strand and minus strand plot elements. The first value will color the plus strand plot elements and the second label will color the minus strand plot elements. Default value is fill = c("#669fd9", "#abcc8e").
geneOrder	An ordered character vector of gene names to prioritize when labeling genes.
geneHighlights	A two-column dataframe with a column named "gene" containing gene names as strings to highlight and a named column "color" containing corresponding highlight colors.
geneBackground	If geneHighlights is given, a character value indicating the color for genes that are not highlighted.
strandLabels	A logical value indicating whether to include + and - strand labels to the left of the gene track.
stroke	A numeric value indicating the stroke width for gene 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 genes plot x-location.
y	A numeric, unit object, or character containing a "b" combined with a numeric value specifying genes plot y-location. The character value will place the genes 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 genes plot width.
height	A numeric or unit object specifying genes plot height.
just	Justification of genes 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 gene track can be placed on a page by providing plot placement parameters:

plotGenes(chrom, chromstart = NULL, chromend = NULL,
            x, y, width, height, just = c("left", "top"),
            default.units = "inches")

This function can be used to quickly plot an unnannotated gene track by ignoring plot placement parameters:

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

Genomic annotation information is acquired through TxDb and OrgDb-class packages, as determined through the assembly parameter. To avoid overcrowding of gene name labels, plotted gene labels are by default prioritized according to citation counts.

Value

Returns a genes 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")

## Set genomic coordinates
paramssmall <- pgParams(
    chrom = "chr8",
    chromstart = 1, chromend = 3000000,
    assembly = "hg19", width = 7
)
paramsbig <- pgParams(
    chrom = "chr8",
    chromstart = 1, chromend = 146364022,
    assembly = "hg19", width = 7
)
## Set colors
cols <- c("#41B6C4", "#225EA8")

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

## Plot genes big
genesPlot <- plotGenes(
    params = paramsbig, fill = cols,
    fontcolor = cols,
    x = 0.25, y = 0.25, height = 0.75,
    just = c("left", "top"),
    default.units = "inches"
)

## Annotate genome label
annoGenomeLabel(
    plot = genesPlot, x = 0.25, y = 1.0,
    scale = "Mb", just = c("left", "top")
)

## Plot genes small
genesPlot <- plotGenes(
    params = paramssmall,
    geneHighlights = data.frame(
        "gene" = c("DLGAP2"),
        "color" = c("#225EA8")
    ),
    geneBackground = "grey",
    x = 0.25, y = 2.25, height = 0.75,
    just = c("left", "top"), default.units = "inches"
)

## Annotate genome label
annoGenomeLabel(
    plot = genesPlot, x = 0.25, y = 3.0, scale = "Mb",
    just = c("left", "top")
)

## Hide page guides
pageGuideHide()

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