ArchRBrowser: Launch ArchR Genome Browser
In haibol2016/ArchR_debug: Analyzing single-cell regulatory chromatin in R.

ArchRBrowser

R Documentation

Launch ArchR Genome Browser

Description

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.

Usage

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.