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