Plot ATAC-RNA scOptMatch pairs — plotPairs • FigR

Function to plot ATAC-RNA pairs in a joint embedding space (.e.g 2D UMAP of both ATAC and RNA cells)

Usage

plotPairs(ATAC, RNA, umap.df, max.show = 300, seed = 123, pairPointSize = 1)

ATAC: character vector of the ATAC barcodes returned in the resulting pairing data frame returned by the cell_pairing function
RNA: character vector of the RNA barcodes returned in the resulting pairing data frame returned by the cell_pairing function
umap.df: data.frame that has the ATAC/RNA co-embedding UMAP 1/2 coordinates in the first and second columns, respectively. Must have valid ATAC and RNA barcodes as row names, which will be used to subset pairs
max.show: numeric specifying the maximum number of pairs to limit plotting to. Default is 300 (choose fewer for better visibility if the UMAP is crowded)
seed: numeric specifying a random seed to set for sampling pairs (for reproducibility). Default is 123
pairPointSize: scatter plot point size. Default is 1

a ggplot scatter plot with user-provided coordinates, highlighting ATAC-RNA pairs

Vinay Kartha