ArchRBrowser: Launch ArchR Genome Browser

In GreenleafLab/ArchR: Analyzing single-cell regulatory chromatin in R.

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. 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.

Usage

ArchRBrowser(
  ArchRProj = NULL,
  features = getPeakSet(ArchRProj),
  loops = getCoAccessibility(ArchRProj),
  sampleLabels = "Sample",
  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().
sampleLabels	The name of a column in cellColData to use to identify samples. In most cases, this parameter should be left as NULL and you should only use this parameter if you do not want to use the default sample labels stored in cellColData$Sample. However, if your individual Arrow files do not map to individual samples, then you should set this parameter to accurately identify your samples. This is the case in (for example) multiplexing applications where cells from different biological samples are mixed into the same reaction and demultiplexed based on a lipid barcode or genotype.
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)`

GreenleafLab/ArchR documentation built on Feb. 21, 2025, 3:05 p.m.