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geom_annotation

Source: R/geom-annotation.R
geom_annotation.Rd

A ggplot2 geom for gene model tracks.

Usage

geom_annotation(
  mapping = NULL,
  data = NULL,
  stat = StatAnnotation,
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE,
  ...,
  txdb = NULL,
  tx2gene = NULL,
  gtf_path = NULL,
  width_ratio = 1/50,
  spacing_ratio = 1/3,
  maxgap = -1,
  include_ncrna = TRUE,
  style = c("basic", "arrow"),
  gene_symbols = NULL,
  chrom_prefix = TRUE,
  fontsize = 10,
  colour = "#48CFCB",
  fill = "#48CFCB",
  draw_boundary = TRUE,
  boundary_colour = "black",
  linetype = "dashed"
)

Arguments

mapping

Set of aesthetic mappings created by aes(). If specified and inherit.aes = TRUE (the default), it is combined with the default mapping at the top level of the plot. You must supply mapping if there is no plot mapping.

data

The data to be displayed in this layer. There are three options:

If NULL, the default, the data is inherited from the plot data as specified in the call to ggplot().

A data.frame, or other object, will override the plot data. All objects will be fortified to produce a data frame. See fortify() for which variables will be created.

A function will be called with a single argument, the plot data. The return value must be a data.frame, and will be used as the layer data. A function can be created from a formula (e.g. ~ head(.x, 10)).

stat

The statistical transformation to use on the data for this layer. When using a geom_*() function to construct a layer, the stat argument can be used the override the default coupling between geoms and stats. The stat argument accepts the following:

  • A Stat ggproto subclass, for example StatCount.

  • A string naming the stat. To give the stat as a string, strip the function name of the stat_ prefix. For example, to use stat_count(), give the stat as "count".

  • For more information and other ways to specify the stat, see the layer stat documentation.

position

A position adjustment to use on the data for this layer. This can be used in various ways, including to prevent overplotting and improving the display. The position argument accepts the following:

  • The result of calling a position function, such as position_jitter(). This method allows for passing extra arguments to the position.

  • A string naming the position adjustment. To give the position as a string, strip the function name of the position_ prefix. For example, to use position_jitter(), give the position as "jitter".

  • For more information and other ways to specify the position, see the layer position documentation.

na.rm

If FALSE, the default, missing values are removed with a warning. If TRUE, missing values are silently removed.

show.legend

logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes. It can also be a named logical vector to finely select the aesthetics to display.

inherit.aes

If FALSE, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. borders().

...

Parameters to be ignored.

txdb

The TxDb object. Default is NULL.

tx2gene

An optional data frame or tibble that maps transcript information to gene information. It should include the following columns:

  • chrom: Chromosome number or name.

  • gene_id: Entrez gene ID.

  • gene_symbol: Common symbol or name of the gene.

  • tx_id: Entrez transcript ID.

  • tx_name: Name of the transcript.

  • gene_type: Type or classification of the gene.

  • tx_type: Type or classification of the transcript.

gtf_path

The path to the GTF file, which is used to generate txdb and tx2gene. Generated files are saved in the cache directory. Default is NULL.

width_ratio

The ratio of the width of each gene model track relative to the height of the Hi-C plot. Default is 1/50.

spacing_ratio

The ratio of the spacing between two gene model tracks. Default is 1/3.

maxgap

The maximum gap between genes to be drawn in the same line. Default is -1.

include_ncrna

Whether to include ncRNA or not. Default is TRUE.

style

The style of the gene model track, which can be "basic" or "arrow". Default is "basic".

gene_symbols

A character vector of gene symbols to be included only. Default is NULL.

chrom_prefix

Whether the input data has chromosome names with prefix 'chr' or not. Default is TRUE.

fontsize

The font size of the gene symbols. Default is 10.

colour

The color of the gene model track. Default is "#48CFCB".

fill

The fill color of the gene model track. Default is "#48CFCB".

draw_boundary

Whether to draw the boundary line or not when plotting multiple chromosomes. Default is TRUE.

boundary_colour

The color of the boundary line. Default is "black".

linetype

The line type of the boundary line. Default is "dashed".

Value

A ggplot object.

Details

Requires the following aesthetics:

  • seqnames1

  • start1

  • end1

  • seqnames2

  • start2

  • end2

Examples

if (FALSE) { # \dontrun{
library(gghic)
library(ggplot2)
library(dplyr)
library(HiCExperiment)
library(InteractionSet)
library(scales)
library(glue)
library(rappdirs)

dir_cache <- user_cache_dir(appname = "gghic")
url_file <- paste0(
  "https://raw.githubusercontent.com/mhjiang97/gghic-data/refs/heads/",
  "master/cooler/chr4_11-5kb.cool"
)
path_file <- glue("{dir_cache}/chr4_11-5kb.cool")
download.file(url_file, path_file)

hic <- path_file |>
  CoolFile() |>
  import()

gis <- interactions(hic)
gis$score <- log10(gis$balanced)
x <- as_tibble(gis)
scores <- x$score[pairdist(gis) != 0 & !is.na(pairdist(gis) != 0)]
scores <- scores[!is.na(scores) & !is.infinite(scores)]
x$score <- oob_squish(x$score, c(min(scores), max(scores)))

p <- x |>
  filter(
    seqnames1 == "chr11", seqnames2 == "chr11",
    center1 > 67000000, center1 < 67100000,
    center2 > 67000000, center2 < 67100000
  ) |>
  ggplot(
    aes(
      seqnames1 = seqnames1, start1 = start1, end1 = end1,
      seqnames2 = seqnames2, start2 = start2, end2 = end2,
      fill = score
    )
  ) +
  geom_hic()

path_gtf <- glue("{dir_cache_gghic}/gencode-chr4_11.gtf.gz")

p + geom_annotation(gtf_path = path_gtf, style = "basic", maxgap = 100000)
} # }