Plot the fragment size distribution for each sample

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

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.