bb_cite_umap: Plot a UMAP Showing Cite-Seq Antibody Binding

In blaserlab/blaseRtools: R Tools for Blaser Lab Data Analysis

Plot a UMAP Showing Cite-Seq Antibody Binding

Description

Requires a cds with an alt experiment established. Use bb_split_citeseq to generate this and to normalize binding data using the CLR method. Returns a ggplot.

Usage

bb_cite_umap(
  cds,
  antibody,
  assay = "CLR_counts",
  cell_size = 1,
  alpha = 1,
  alt_dim_x = NULL,
  alt_dim_y = NULL,
  plot_title = NULL,
  color_legend_title = NULL,
  order = TRUE,
  rescale = NULL,
  ncol = NULL
)

Arguments

cds	The cds with an "Antibody Capture" alt experiment to plot.
antibody	The name of the antibody to plot. Equivalent to gene_short_name. Accepts a character vector.
assay	The binding assay to use, Default: "CLR_counts"
cell_size	Size of points to plot, Default: 1
alpha	Alpha for the plotted points, Default: 1
alt_dim_x	Alternate/reference dimensions to plot by.
alt_dim_y	Alternate/reference dimensions to plot by.
plot_title	Optional title for the plot, Default: NULL
color_legend_title	Optional title for the color scale., Default: NULL
order	Whether or not to order cells by gene expression. When ordered, non-expressing cells are plotted first, i.e. on the bottom. Default: TRUE
rescale	Optional redefinition of the color scale, Default: NULL
ncol	If specified, the number of columns for facet_wrap, Default: NULL

Value

a ggplot

See Also

reducedDims

blaserlab/blaseRtools documentation built on April 14, 2025, 6:04 p.m.