Launch ArchR Genome Browser — ArchRBrowser • ArchR

This function will open an interactive shiny session in style of a browser track. It allows for normalization of the signal which enables direct comparison across samples. Note that the genes displayed in this browser are derived from your geneAnnotation (i.e. the BSgenome object you used) so they may not match other online genome browsers that use different gene annotations.

ArchRBrowser(
  ArchRProj = NULL,
  features = getPeakSet(ArchRProj),
  loops = getCoAccessibility(ArchRProj),
  minCells = 25,
  baseSize = 10,
  borderWidth = 0.5,
  tickWidth = 0.5,
  facetbaseSize = 12,
  geneAnnotation = getGeneAnnotation(ArchRProj),
  browserTheme = "cosmo",
  threads = getArchRThreads(),
  verbose = TRUE,
  logFile = createLogFile("ArchRBrowser")
)

Arguments

ArchRProj: An ArchRProject object.
features: A GRanges object containing the "features" to be plotted via the "featureTrack". This should be thought of as a bed track. i.e. the set of peaks obtained using getPeakSet(ArchRProj)).
loops: A GRanges object containing the "loops" to be plotted via the "loopTrack". This GRanges object start represents the center position of one loop anchor and the end represents the center position of another loop anchor. A "loopTrack" draws an arc between two genomic regions that show some type of interaction. This type of track can be used to display chromosome conformation capture data or co-accessibility links obtained using getCoAccessibility().
minCells: The minimum number of cells contained within a cell group to allow for this cell group to be plotted. This argument can be used to exclude pseudo-bulk replicates generated from low numbers of cells.
baseSize: The numeric font size to be used in the plot. This applies to all plot labels.
borderWidth: The numeric line width to be used for plot borders.
tickWidth: The numeric line width to be used for axis tick marks.
facetbaseSize: The numeric font size to be used in the facets (gray boxes used to provide track labels) of the plot.
geneAnnotation: The geneAnnotation object to be used for plotting the "geneTrack" object. See createGeneAnnotation() for more info.
browserTheme: A shinytheme from shinythemes for viewing the ArchR Browser. If not installed this will be NULL. To install try devtools::install_github("rstudio/shinythemes").
threads: The number of threads to use for parallel execution.
verbose: A boolean value that determines whether standard output should be printed.
logFile: The path to a file to be used for logging ArchR output.

Examples


proj <- getTestProject()

#Launch Browser with `ArchRBrowser(proj)`