Plotting functions

#' @description

Usage

geom_aggrcoverage(
  mapping = NULL,
  data = NULL,
  ...,
  unit = c("kb", "Mb", "b"),
  ci = TRUE,
  grid = FALSE,
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

geom_coverage(
  mapping = NULL,
  data = NULL,
  ...,
  type = c("area", "line"),
  unit = c("kb", "Mb", "b"),
  grid = FALSE,
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

scale_y_coverage()

scale_x_genome(unit = c("kb", "Mb", "b"))

Arguments

mapping

Aesthetics for geom_*. By default, no color/fill aesthetic is specified, but they can be assigned to a variable with mapping = aes(...). Note that x and y are automatically filled.

data

Data frame passed to geom_*. Typically a CoverageExperiment object (expanded to a tibble) or a AggregatedCoverage object.

..., na.rm, show.legend, inherit.aes

Argument passed to ggplot internal functions

unit

Rounding of x axis (any of c('b', 'kb', 'Mb')).

ci

Should the confidence interval be plotted by geom_aggrcoverage()? (default: TRUE)

grid

Should the plot grid by displayed? (default: FALSE).

type

Choose between "line" and "area" style for geom_coverage().

Value

A ggplot object`

Details

Plotting functions for tidyCoverage objects

Examples

library(rtracklayer)
library(plyranges)
library(ggplot2)
library(purrr)
TSSs_bed <- system.file("extdata", "TSSs.bed", package = "tidyCoverage")
features <- list(
    TSS_fwd = import(TSSs_bed) |> filter(strand == '+'), 
    TSS_rev = import(TSSs_bed) |> filter(strand == '-'), 
    conv_sites = import(system.file("extdata", "conv_transcription_loci.bed", package = "tidyCoverage"))
)
tracks <- list(
    RNA_fwd = system.file("extdata", "RNA.fwd.bw", package = "tidyCoverage"),
    RNA_rev = system.file("extdata", "RNA.rev.bw", package = "tidyCoverage"), 
    Scc1 = system.file("extdata", "Scc1.bw", package = "tidyCoverage")
) |> map(import, as = 'Rle')
ce <- CoverageExperiment(tracks, features, width = 5000, center = TRUE, scale = TRUE)
ac <- aggregate(ce) 

#############################################################################
## 1. Plotting aggregated coverage
#############################################################################

ac |> 
    as_tibble() |> 
    ggplot() + 
    geom_aggrcoverage(aes(col = track)) + 
    facet_grid(track ~ features) + 
    geom_vline(xintercept = 0, color = 'black', linetype = 'dashed', linewidth = 0.5)


#############################################################################
## 2. Plotting track coverages over individual loci
#############################################################################

ce2 <- CoverageExperiment(
    tracks, 
    GRangesList(list(locus1 = "II:400001-455000", locus2 = "IV:720001-775000")), 
    window = 50
)
expand(ce2) |> 
    mutate(coverage = ifelse(track != 'Scc1', scales::oob_squish(coverage, c(0, 50)), coverage)) |>
    ggplot() + 
    geom_coverage(aes(fill = track)) + 
    facet_grid(track~features, scales = 'free')