R: Plot sequence motifs

plot_motif_logo {ALPS}

R Documentation

Plot sequence motifs

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')

[Package ALPS version 1.0.0 Index]