plot_motif_occurrence: Plot motif occurrence

In jhammelman/spatzie: Identification of enriched motif pairs from chromatin interaction data

Plot motif occurrence

Description

Plots a histogram of motif values (either counts, instances, or scores) for anchor 1 and anchor 2 regions.

Usage

plot_motif_occurrence(
  interaction_data,
  method = c("counts", "instances", "scores")
)

Arguments

interaction_data	an interactionData object of paired genomic regions
method	way to interpret motif matching for each anchor region as "counts" number of motifs per region, "instances" motif present or absent each region, or "scores" maximum motif PWM match score for each region

Value

plot containing histogram for each anchor

Author(s)

Jennifer Hammelman

Examples

## Not run: 
genome_id <- "BSgenome.Mmusculus.UCSC.mm9"
if (!(genome_id %in% rownames(utils::installed.packages()))) {
  BiocManager::install(genome_id, update = FALSE, ask = FALSE)
}
genome <- BSgenome::getBSgenome(genome_id)

motifs_file <- system.file("extdata/motifs_subset.txt.gz",
                           package = "spatzie")
motifs <- TFBSTools::readJASPARMatrix(motifs_file, matrixClass = "PFM")

yy1_pd_interaction <- scan_motifs(spatzie::interactions_yy1, motifs, genome)
yy1_pd_interaction <- filter_motifs(yy1_pd_interaction, 0.4)
plot_motif_occurrence(yy1_pd_interaction,"counts")

## End(Not run)

plot_motif_occurrence(spatzie::anchor_pair_example_score)

jhammelman/spatzie documentation built on Feb. 8, 2024, 8:50 a.m.