view_motifs {universalmotif} | R Documentation |
Show sequence logo. If given a list of more than one motif, then the motifs are aligned with the first in the list.
view_motifs(motifs, use.type = "ICM", method = "MPCC", tryRC = TRUE, min.overlap = 6, min.mean.ic = 0.5, relative_entropy = FALSE, normalise.scores = FALSE, ...)
motifs |
See |
use.type |
|
method |
|
tryRC |
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min.overlap |
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min.mean.ic |
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relative_entropy |
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normalise.scores |
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... |
Additional options for |
Since the ggseqlogo package can only plot individual
characters and not strings, plotting the multifreq
slot is not
supported. See the examples
section for plotting the multifreq
slot using the Logolas package.
A ggplot object.
Benjamin Jean-Marie Tremblay, b2tremblay@uwaterloo.ca
Dey KK, Xie D, Stephens M (2017). “A new sequence logo plot to highlight enrichment and depletion.” bioRxiv, p.226597.
Wagih O (2017). ggseqlogo: A 'ggplot2' Extension for Drawing Publication-Ready Sequence Logos. R package version 0.1, https://CRAN.R-project.org/package=ggseqlogo.
compare_motifs()
, add_multifreq()
## plotting multifreq motifs: ## Not run: motif <- create_motif() motif <- add_multifreq(motif, sample_sites(motif)) Logolas::logomaker(motif["multifreq"][[as.character(2)]], type = "Logo", color_type = "per_symbol") ## End(Not run)