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
Value
Returns a ggplot object
Examples
# \donttest{
fpath <- system.file("extdata", "fragments.tsv.gz", package="Signac")
Fragments(atac_small) <- CreateFragmentObject(
path = fpath,
cells = colnames(atac_small),
validate.fragments = FALSE
)
#> Computing hash
FragmentHistogram(object = atac_small, region = "chr1-10245-780007")
#> Warning: Removed 4 rows containing missing values or values outside the scale range
#> (`geom_bar()`).
# }