plotBrowserTrack: Plot an ArchR Region Track
In haibol2016/ArchR_debug: Analyzing single-cell regulatory chromatin in R.

plotBrowserTrack

R Documentation

Plot an ArchR Region Track

Description

This function will plot the coverage at an input region in the style of a browser track. It allows for normalization of the signal which enables direct comparison across samples.

Usage

plotBrowserTrack(
  ArchRProj = NULL,
  region = NULL,
  groupBy = "Clusters",
  useGroups = NULL,
  plotSummary = c("bulkTrack", "featureTrack", "loopTrack", "geneTrack"),
  sizes = c(10, 1.5, 3, 4),
  features = getPeakSet(ArchRProj),
  loops = getCoAccessibility(ArchRProj),
  geneSymbol = NULL,
  useMatrix = NULL,
  log2Norm = TRUE,
  upstream = 50000,
  downstream = 50000,
  tileSize = 250,
  minCells = 25,
  normMethod = "ReadsInTSS",
  threads = getArchRThreads(),
  ylim = NULL,
  pal = NULL,
  baseSize = 7,
  scTileSize = 0.5,
  scCellsMax = 100,
  borderWidth = 0.4,
  tickWidth = 0.4,
  facetbaseSize = 7,
  geneAnnotation = getGeneAnnotation(ArchRProj),
  title = "",
  verbose = TRUE,
  logFile = createLogFile("plotBrowserTrack")
)

Arguments

`ArchRProj`	An `ArchRProject` object.
`region`	A `GRanges` region that indicates the region to be plotted. If more than one region exists in the `GRanges` object, all will be plotted. If no region is supplied, then the `geneSymbol` argument can be used to center the plot window at the transcription start site of the supplied gene.
`groupBy`	A string that indicates how cells should be grouped. This string corresponds to one of the standard or user-supplied `cellColData` metadata columns (for example, "Clusters"). Cells with the same value annotated in this metadata column will be grouped together and the average signal will be plotted.
`useGroups`	A character vector that is used to select a subset of groups by name from the designated `groupBy` column in `cellColData`. This limits the groups to be plotted.
`plotSummary`	A character vector containing the features to be potted. Possible values include "bulkTrack" (the ATAC-seq signal), "scTrack" (scATAC-seq signal), "featureTrack" (i.e. the peak regions), "geneTrack" (line diagrams of genes with introns and exons shown. Blue-colored genes are on the minus strand and red-colored genes are on the plus strand), and "loopTrack" (links between a peak and a gene).
`sizes`	A numeric vector containing up to 3 values that indicate the sizes of the individual components passed to `plotSummary`. The order must be the same as `plotSummary`.
`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()`.
`geneSymbol`	If `region` is not supplied, plotting can be centered at the transcription start site corresponding to the gene symbol(s) passed here.
`useMatrix`	If supplied geneSymbol, one can plot the corresponding GeneScores/GeneExpression within this matrix. I.E. "GeneScoreMatrix"
`log2Norm`	If supplied geneSymbol, Log2 normalize the corresponding GeneScores/GeneExpression matrix before plotting.
`upstream`	The number of basepairs upstream of the transcription start site of `geneSymbol` to extend the plotting window. If `region` is supplied, this argument is ignored.
`downstream`	The number of basepairs downstream of the transcription start site of `geneSymbol` to extend the plotting window. If `region` is supplied, this argument is ignored.
`tileSize`	The numeric width of the tile/bin in basepairs for plotting ATAC-seq signal tracks. All insertions in a single bin will be summed.
`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.
`normMethod`	The name of the column in `cellColData` by which normalization should be performed. The recommended and default value is "ReadsInTSS" which simultaneously normalizes tracks based on sequencing depth and sample data quality.
`threads`	The number of threads to use for parallel execution.
`ylim`	The numeric quantile y-axis limit to be used for for "bulkTrack" plotting. If not provided, the y-axis limit will be c(0, 0.999).
`pal`	A custom palette (see `paletteDiscrete` or `ArchRPalettes`) used to override coloring for groups.
`baseSize`	The numeric font size to be used in the plot. This applies to all plot labels.
`scTileSize`	The width of the tiles in scTracks. Larger numbers may make cells overlap more. Default is 0.5 for about 100 cells.
`scCellsMax`	The maximum number of cells for scTracks.
`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.
`title`	The title to add at the top of the plot next to the plot's genomic coordinates.
`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.