plotFragmentSizes: Plot the fragment size distribution for each sample

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

Plot the fragment size distribution for each sample

Description

This function will plot a fragment size distribution for each sample. Only cells in the ArchRProject are used when making this plot.

Usage

plotFragmentSizes(
  ArchRProj = NULL,
  groupBy = "Sample",
  chromSizes = getChromSizes(ArchRProj),
  maxSize = 750,
  pal = NULL,
  returnDF = FALSE,
  threads = getArchRThreads(),
  logFile = createLogFile("plotFragmentSizes")
)

Arguments

ArchRProj	An ArchRProject object.
groupBy	The name of the column in cellColData to use for grouping cells together for summarizing.
chromSizes	A GRanges object of the chromosome lengths. See getChromSizes for more info.
maxSize	The maximum fragment size (in basepairs) to be included when plotting the fragment size distribution.
pal	A color palette representing the groups from groupBy in fragment size plot.
returnDF	A boolean value that indicates whether to return a data.frame containing the plot information instead of plotting the fragment size distribution.
threads	An integer specifying the number of threads to use for calculation. By default this uses the number of threads set by addArchRThreads().
logFile	The path to a file to be used for logging ArchR output.

Examples

# Get Test ArchR Project
proj <- getTestProject()

# Plot Frag Sizes
p <- plotFragmentSizes(proj, groupBy = "Clusters")

# PDF
plotPDF(p, name = "Frag-Sizes", ArchRProj = proj)

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