Plots: Group Kmers and Represent them as Motif Logos

In TaliaferroLab/FeatureReachR: Extract Enriched Biological Features From RNA-seq Data

Description

Kmers of interest can be collapsed or grouped by their levenshtein distance (>2) to simplify enriched/depleted kmer outputs. These functions help visualize how kmers are grouped as well as provide PWM which can be visualized using ggseqlogo.

Usage

kmer2logo(kmers, title = "")

kmer2tree(kmers, title = "")

Arguments

kmers	character list of kmers of the length.
title	string for plot titles defaults to no title.

Value

a tree, seqotif plots or a named list of PWMs

Functions

• kmer2logo: the tree and all seq logos together

• kmer2tree: the tree of kmers with groups highlighted.

See Also

kmer_compare, ggseqlogo, msaClustalW

Examples

enriched_sixmers <- c("AAGGAA", "ACACAC", "AGAAGG", "AGAGAG", "AGAGGG",
"AGGAAG", "AGGAGG", "AGGGAG", "CACACA", "GAAGGA", "GAGAAG", "GAGAGA",
"GAGGAG", "GAGGGA", "GAGGGG", "GGAAGG", "GGAGGA", "GGAGGG", "GGGAGG")
kmer2logo(enriched_sixmers, "My Plot Title")
kmer2tree(enriched_sixmers, "My Tree Title")
kmer_PWMs <- kmer2PWM(enriched_sixmers)
kmer_PWMs

TaliaferroLab/FeatureReachR documentation built on Aug. 15, 2021, 2:21 p.m.