addAnnotation: Add annotation ranges to a SVbyEye plot.

In daewoooo/SVbyEye: Visualization of genomic structural variants

Add annotation ranges to a SVbyEye plot.

Description

This function takes a ggplot2 object generated using plotMiro function and adds extra annotation on top of query or target coordinates. These ranges are specified in 'annot.gr' object and are visualized either as arrowheads or rectangles.

Usage

addAnnotation(
  ggplot.obj = NULL,
  annot.gr = NULL,
  shape = "arrowhead",
  fill.by = NULL,
  label.by = NULL,
  color.palette = NULL,
  max.colors = 20,
  coordinate.space = "target",
  annotation.group = NULL,
  annotation.level = 0.05,
  offset.annotation = FALSE,
  annotation.label = NULL,
  y.label.id = NULL
)

Arguments

ggplot.obj	A ggplot2 object generated using plotMiro function.
annot.gr	A GRanges-class object with a set of ranges to be added as extra annotation.
shape	A user defined shape ranges in 'annot.gr' are visualized, either 'arrowhead' or 'rectangle'.
fill.by	A name of an extra field present in 'annot.gr' to be used to define color scheme.
label.by	A name of an extra field present in 'annot.gr' to be used as a label over each annotation range.
color.palette	A discrete color palette defined as named character vector (elements = colors, names = discrete levels).
max.colors	A maximum number of discrete color levels for which legend will be reported. If more than that legend will be removed.
coordinate.space	A coordinate space ranges in 'annot.gr' are reported, either 'target', 'query' or 'self'.
annotation.group	A name of an extra field present in 'annot.gr' to be used to connect set of ranges of the same group by a straight black line (Useful to plot exons from one or multiple genes).
annotation.level	A numeric that defines a fraction of y-axis to be the y-axis position for the annotation track (Default : '0.05').
offset.annotation	Set to TRUE if subsequent annotation ranges should be offsetted below and above the midline.
annotation.label	A character string to be used as a label to added annotation track.
y.label.id	A user defined metadata column id within 'annot.gr' that for each annotation range contains corresponding y-axis label.

Value

A ggplot2 object.

Author(s)

David Porubsky

Examples

## Get PAF to plot
paf.file <- system.file("extdata", "test1.paf", package = "SVbyEye")
## Read in PAF
paf.table <- readPaf(paf.file = paf.file, include.paf.tags = TRUE, restrict.paf.tags = "cg")
## Make a plot
plt <- plotMiro(paf.table = paf.table)
## Load target annotation file
target.annot <- system.file("extdata", "test1_target_annot.txt", package = "SVbyEye")
target.annot.df <- read.table(target.annot, header = TRUE, sep = "\t", stringsAsFactors = FALSE)
target.annot.gr <- GenomicRanges::makeGRangesFromDataFrame(target.annot.df)
## Add target annotation as arrowhead
plt <- addAnnotation(ggplot.obj = plt, annot.gr = target.annot.gr, coordinate.space = "target")
## Load query annotation file
query.annot <- system.file("extdata", "test1_query_annot.txt", package = "SVbyEye")
query.annot.df <- read.table(query.annot, header = TRUE, sep = "\t", stringsAsFactors = FALSE)
query.annot.gr <- GenomicRanges::makeGRangesFromDataFrame(query.annot.df)
## Add query annotation as rectangle
addAnnotation(
    ggplot.obj = plt, annot.gr = query.annot.gr, shape = "rectangle",
    coordinate.space = "query"
)
## Add segmental duplication annotation
plt <- plotMiro(paf.table = paf.table)
sd.annot <- system.file("extdata", "test1.sd.annot.RData", package = "SVbyEye")
sd.annot.gr <- get(load(sd.annot))
## Create a custom discrete levels
sd.categ <- findInterval(sd.annot.gr$fracMatch, vec = c(0.95, 0.98, 0.99))
sd.categ <- dplyr::recode(sd.categ, "0" = "<95%", "1" = "95-98%", "2" = "98-99%", "3" = ">=99%")
sd.categ <- factor(sd.categ, levels = c("<95%", "95-98%", "98-99%", ">=99%"))
sd.annot.gr$sd.categ <- sd.categ
## Create a custom color palette
color.palette <- c(
    "<95%" = "gray72", "95-98%" = "gray47", "98-99%" = "#cccc00",
    ">=99%" = "#ff6700"
)
## Add annotation to the plot
addAnnotation(
    ggplot.obj = plt, annot.gr = sd.annot.gr, fill.by = "sd.categ",
    color.palette = color.palette, coordinate.space = "target"
)
## Offset annotation ranges
addAnnotation(
    ggplot.obj = plt, annot.gr = sd.annot.gr, fill.by = "sd.categ",
    color.palette = color.palette, coordinate.space = "target", offset.annotation = TRUE
)
## Add label to the added annotation
addAnnotation(
    ggplot.obj = plt, annot.gr = sd.annot.gr, fill.by = "sd.categ",
    color.palette = color.palette, coordinate.space = "target", annotation.label = "SD"
)

## Add gene-like annotation
test.gr <- GenomicRanges::GRanges(
    seqnames = "target.region",
    ranges = IRanges::IRanges(
        start = c(19000000, 19030000, 19070000),
        end = c(19010000, 19050000, 19090000)
    ),
    ID = "gene1"
)
addAnnotation(
    ggplot.obj = plt, annot.gr = test.gr, coordinate.space = "target",
    shape = "rectangle", annotation.group = "ID", offset.annotation = TRUE,
    fill.by = "ID"
)
## Add gene names
addAnnotation(
    ggplot.obj = plt, annot.gr = test.gr, coordinate.space = "target",
    shape = "rectangle", annotation.group = "ID", offset.annotation = TRUE,
    fill.by = "ID", label.by = "ID"
)

daewoooo/SVbyEye documentation built on Oct. 15, 2024, 6:12 a.m.