FragmentHistogram function

Plot fragment length histogram

Plot the frequency that fragments of different lengths are present for different groups of cells.

FragmentHistogram(
  object,
  assay = NULL,
  region = "chr1-1-2000000",
  group.by = NULL,
  cells = NULL,
  log.scale = FALSE,
  ...
)

Arguments

• object: A Seurat object
• assay: Which assay to use. Default is the active assay.
• region: Genomic range to use. Default is fist two megabases of chromosome 1. Can be a GRanges object, a string, or a vector of strings.
• group.by: Name of one or more metadata columns to group (color) the cells by. Default is the current cell identities
• cells: Which cells to plot. Default all cells
• log.scale: Display Y-axis on log scale. Default is FALSE.
• ...: Arguments passed to other functions

Returns

Returns a ggplot object

Examples

fpath <- system.file("extdata", "fragments.tsv.gz", package="Signac")
Fragments(atac_small) <- CreateFragmentObject(
  path = fpath,
  cells = colnames(atac_small),
  validate.fragments = FALSE
)
FragmentHistogram(object = atac_small, region = "chr1-10245-780007")