bb_plotfootprint: Plot motif footprinting results
In blaserlab/blaseRtools: R Tools for Blaser Lab Data Analysis

bb_plotfootprint

R Documentation

Plot motif footprinting results

Description

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.