ArchRBrowser | R Documentation |
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")
)
ArchRProj |
An |
features |
A |
loops |
A |
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 |
browserTheme |
A |
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. |
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