view_tomtom_hits: Compare top tomtom hits to original motif

In snystrom/dremeR: motif matching, comparison, and de novo discovery using the MEME Suite

Compare top tomtom hits to original motif

Description

Although TomTom does a good job of matching unknown motifs to known motifs, sometimes the top hit is not the correct assignment. It can be useful to manually inspect the hits. This function provides a quick utility to compare matches.

Usage

view_tomtom_hits(results, top_n = "all")

Arguments

results	results data.frame from [runTomTom()]
top_n	number of matched motifs to return in plot (default: "all")

Details

This is intended to be a function used interactively and may not always be the best tool for creating publication-quality figures. Results with matches return ggseqlogo outputs which can be further manipulated using [ggplot2::theme()] calls, but results containing no matches are static plots.

Value

plot of input motif vs the top n number of tomtom matched motifs. If no match found, will plot "No Match". Note: the "No Match" plots are not amenable to ggplot theme() manipulations, while all others are.

Examples

results <- importTomTomXML(system.file("extdata", "tomtom.xml", package = "memes"))
# show top 3 hits
view_tomtom_hits(results, top_n = 3)

snystrom/dremeR documentation built on Oct. 13, 2024, 10:48 p.m.