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.