PlotFootprint function

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.