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, ... )
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 a ggplot object
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")Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.