Plot the footprinting around TF motif sites
Usage
plot_tf_footprint(
fragments,
motif_positions,
cell_groups = rlang::rep_along(cellNames(fragments), "all"),
flank = 250L,
smooth = 0L,
zero_based_coords = !is(genes, "GRanges"),
colors = discrete_palette("stallion"),
return_data = FALSE,
apply_styling = TRUE
)Arguments
- fragments
IterableFragments object
- motif_positions
Coordinate ranges for motifs (must include strand) and have constant width
- cell_groups
Character or factor assigning a group to each cell, in order of
cellNames(fragments)- flank
Number of flanking basepairs to include on either side of the motif
- smooth
(optional) Sparse matrix of dimensions cells x cells with cell-cell distance weights for smoothing.
- zero_based_coords
If true, coordinates start and 0 and the end coordinate is not included in the range. If false, coordinates start at 1 and the end coordinate is included in the range
- return_data
If true, return data from just before plotting rather than a plot.
- apply_styling
If false, return a plot without pretty styling applied
