Plot motif footprinting results

Plot motif footprinting results

PlotFootprint(
  object,
  features,
  assay = NULL,
  group.by = NULL,
  split.by = NULL,
  idents = NULL,
  label = TRUE,
  repel = TRUE,
  show.expected = TRUE,
  normalization = "subtract",
  label.top = 3,
  label.idents = NULL
)

Arguments

object

A Seurat object

features

A vector of features to plot

assay

Name of assay to use

group.by

A grouping variable

split.by

A metadata variable to split the plot by. For example, grouping by "celltype" and splitting by "batch" will create separate plots for each celltype and batch.

idents

Set of identities to include in the plot

label

TRUE/FALSE value to control whether groups are labeled.

repel

Repel labels from each other

show.expected

Plot the expected Tn5 integration frequency below the main footprint plot

normalization

Method to normalize for Tn5 DNA sequence bias. Options are "subtract", "divide", or NULL to perform no bias correction.

label.top

Number of groups to label based on highest accessibility in motif flanking region.

label.idents

Vector of identities to label. If supplied, label.top will be ignored.