plot_motif_logo: Plot sequence motifs

In ALPS: AnaLysis routines for ePigenomicS data

Description

Function to plot transscription factor motif logos in two different styles, bar plot or logo plot. It supports motif formats from different databases e.g. JASPAR, MEME, TRANSFAC, HOMER and PFM

Usage

plot_motif_logo(motif_path, database = NULL, plot_type = "bar")

Arguments

motif_path	path to motif file, default NULL
database	database name from which motif has taken, default NULL
plot_type	either bar or logo, default bar

Value

ggplot2 object

Examples

## examplr motif file paths
myc_meme <- system.file('extdata/motifs', 'MA0147.2.meme', package = 'ALPS', mustWork = TRUE)
myc_jaspar <- system.file('extdata/motifs', 'MA0147.2.jaspar', package = 'ALPS', mustWork = TRUE)
myc_transfac <- system.file('extdata/motifs', 'MA0147.2.transfac', package = 'ALPS', mustWork = TRUE)
myc_homer <- system.file('extdata/motifs', 'cmyc.homer', package = 'ALPS', mustWork = TRUE)
myc_pfm <- system.file('extdata/motifs', 'MA0147.2.pfm', package = 'ALPS', mustWork = TRUE)

## plot motifs
plot_motif_logo(motif_path = myc_homer, database = 'homer', plot_type = 'logo')

ALPS documentation built on Nov. 8, 2020, 5:52 p.m.