plot_motif_logo {ALPS} | R Documentation |
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
plot_motif_logo(motif_path, database = NULL, plot_type = "bar")
motif_path |
path to motif file, default |
database |
database name from which motif has taken, default |
plot_type |
either |
ggplot2
object
## 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')