Interactive IGV visualisation (Shiny + igvShiny) of differential regions

Launches a Shiny app with an embedded IGV browser and an interactive table listing differentially-bound regions (from `differential_binding()` or `differential_accessibility()` results). Clicking on a region in the table will pan IGV to that locus. Sample coverage and region tracks are loaded as quantitative/annotation tracks. A dedicated "Save as SVG" button is provided to export the current IGV view.

Usage

browse_igv_regions(
  diff_results,
  samples = NULL,
  use_unique_ids = TRUE,
  average_tracks = FALSE,
  export_data_archive = NULL,
  colour_cond1 = "#ff6600",
  colour_cond2 = "#2288dd",
  use_genome = NULL,
  padding_width = 20000,
  trackHeight = 65,
  peakColour = "darkgreen",
  trackColour = "#6666ff",
  host = "localhost",
  port = NULL
)

Arguments

diff_results: A `DamIDResults` object, as returned by `differential_binding()` or `differential_accessibility()`.
samples: Optional character vector of sample names to display (default: all in dataset).
use_unique_ids: Logical. When `TRUE` (default), simplified unique sample names will be displayed. Set as `FALSE` to use the full sample file names from loading.
average_tracks: Logical. If `TRUE`, displays the average signal for each condition instead of individual replicate tracks. (Default: `FALSE`)
export_data_archive: Character or NULL. If a filename is provided (e.g. "my_data"), the function exports all IGV tracks as a zip archive ("my_data.zip") and exits without launching the browser. (Default: NULL)
colour_cond1, colour_cond2: Colours for differentially-enriched region tracks.
use_genome: IGV genome name (inferred from peak annotations if not provided).
padding_width: Width to pad browser viewbox on either side of the peak (Default: 20000)
trackHeight: Height of bedGraph tracks (Default: 65)
peakColour: Colour for significant peaks track (Default: "darkgreen")
trackColour: Colour for bedGraph tracks (Default: "#6666ff")
host: Hostname for the server location (Default: "localhost").
port: Port for connection (if NULL (default) the port is assigned by Shiny).

Value

Invisibly returns the Shiny app object if launching the browser, or the path to the zip archive if exporting data.

Details

Alternatively, if `export_data_archive` is provided, the function will bypass the browser and save all tracks (including averaged tracks) as a zip archive of bedGraph and BED files.

Examples

if (FALSE) { # \dontrun{
if (isTRUE(curl::has_internet()) && interactive()) {
# This example launches an interactive Shiny app in a web browser

.generate_example_results <- function() {
    mock_genes_gr <- GenomicRanges::GRanges(
        seqnames = S4Vectors::Rle("2L", 7),
        ranges = IRanges::IRanges(
            start = c(1000, 2000, 3000, 5000, 6000, 7000, 8000),
            end = c(1500, 2500, 3500, 5500, 6500, 7500, 20000000)
        ),
        gene_id = c("FBgn001", "FBgn002", "FBgn003", "FBgn004", "FBgn005", "FBgn006", "FBgn007"),
        gene_name = c("geneA", "geneB", "geneC", "geneD", "geneE", "geneF", "LargeTestGene")
    )
    data_dir <- system.file("extdata", package = "damidBind")
    loaded_data <- load_data_peaks(
        binding_profiles_path = data_dir,
        peaks_path = data_dir,
        ensdb_genes = mock_genes_gr,
        quantile_norm = TRUE
    )
    diff_results <- differential_binding(
        loaded_data,
        cond = c("L4 Neurons" = "L4",
                 "L5 Neurons" = "L5")
    )
    return(diff_results)
}
diff_results <- .generate_example_results()

# Launch the interactive browser
browse_igv_regions(diff_results)

# Export data instead of launching browser
browse_igv_regions(diff_results, export_data_archive = "L4_vs_L5_tracks")
}
} # }