Skip to contents

Plot motif footprinting results

Usage

bb_plotfootprint(
  object,
  features,
  alt_main_title = NULL,
  alt_color_title = NULL,
  legend_pos = "right",
  colorscale = NULL,
  assay = NULL,
  group.by = NULL,
  idents = NULL,
  label = TRUE,
  repel = TRUE,
  show.expected = TRUE,
  normalization = "subtract",
  label.top = 3,
  label.idents = NULL,
  fontsize = 14,
  linesize = 0.2
)

Arguments

object

A Seurat object

features

A vector of features to plot

alt_main_title

Alternative title for the main plot. Accepts markdown.

alt_color_title

Alternative title for the color scale

legend_pos

Position to place the legend

colorscale

Named vector of colors to apply to the top plot.

assay

Name of assay to use

group.by

A grouping variable

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,

fontsize

Theme font size

linesize

Size to draw the footprint lines label.top will be ignored.