Plot a scatter of gene expression vs an atac profile

Usage

plot_atac_rna(
  atac_mc,
  gene,
  atac_promoter = gene,
  mc_rna = NULL,
  peak = NULL,
  max_dist_to_promoter_peak = 500,
  normalize_atac = TRUE,
  eps_rna = 0.00001,
  tss_intervals = "intervs.global.tss",
  plot_object_id = TRUE
)

Arguments

atac_mc: a McPeaks object
gene: name of the gene to plot
atac_promoter: name of the promoter to plot. By default this would be the rna gene gene.
mc_rna: a metacell1 'mc' object or a metacells metacell UMI matrix (a matrix where each row is a gene and each column is a metacell). Can be NULL if atac_mc already contains the gene expression data (added by add_mc_rna).
peak: name of the peak to plot. If NULL - the promoter of atac_promoter would be shown. You can get the peak names from atac@peaks$peak_name
max_dist_to_promoter_peak: how far from gene's TSS to search for promoter-proximal peaks. Default: 500
normalize_atac: whether to use normalized atac profiles (default: TRUE)
eps_rna: added regularization when calculating log expression (Default: 1e-5). Promoter ATAC signal has been observed empirically to often be linearly correlated with log of gene expression.
tss_intervals: name of the intervals set containing the TSSs
plot_object_id: plot the object id of the atac_mc object in the bottom left corner of the plot (default: TRUE)

Value

a ggplot object with the scatter plot

Examples

if (FALSE) {
p1 <- plot_atac_rna(atac_mc = pbmc_atac_mc, mc_rna = pbmc_rna_mc, gene = "CD4")

p2 <- plot_atac_rna(atac_mc = pbmc_atac_mc, mc_rna = pbmc_rna_mc, gene = "CD4", atac_promoter = "CD8")

# Plot gene vs some peak of interest
peak <- atac_mc@peaks[1]$peak_name
p3 <- plot_atac_rna(atac_mc = pbmc_atac_mc, mc_rna = pbmc_rna_mc, gene = "CD4", peak = peak)
}