motifLocation: Extract and Visualize Motif Information from MEME Software

In ggmotif: Extract and Visualize Motif Information from MEME Software

Extract and Visualize Motif Information from MEME Software

Description

motifLocation Visualize motif location in a specificial sequences..

Arguments

data	A data frame file from getMotifFromXML function.
tree.path	A file path of the correponding phylogenetic tree. The IDs of the phylogenetic tree must be same as the IDs of sequences used to identify motifs using MEME.

Value

Return a plot

Author(s)

Xiang LI <[e-mail]>

Examples

# without phylogenetic tree
filepath <- system.file("examples", "meme.xml", package = "ggmotif")
motif_extract <- getMotifFromMEME(data = filepath, format="xml")
motif_plot <- motifLocation(data = motif_extract)

# with phylogenetic tree
filepath <- system.file("examples", "meme.xml", package = "ggmotif")
treepath <- system.file("examples", "ara.nwk", package="ggmotif")
motif_extract <- getMotifFromMEME(data = filepath, format="xml")
motif_plot <- motifLocation(data = motif_extract, tree = treepath)

ggmotif documentation built on Aug. 11, 2022, 5:11 p.m.