plotPairs: Plot ATAC-RNA scOptMatch pairs

In buenrostrolab/FigR: Functional Inference of Gene Regulation (FigR) using paired single cell ATAC-seq and RNA-seq data

Plot ATAC-RNA scOptMatch pairs

Description

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)

Arguments

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

Value

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

Author(s)

Vinay Kartha

buenrostrolab/FigR documentation built on Feb. 10, 2023, 11:26 a.m.