view_motifs {universalmotif} | R Documentation

## Plot motif logos.

### Description

Show sequence logo. If given a list of more than one motif, then the motifs are aligned with the first in the list.

### Usage

    view_motifs(motifs, use.type = "ICM", method = "MPCC", tryRC = TRUE,
      min.overlap = 6, min.mean.ic = 0.5, relative_entropy = FALSE,
      normalise.scores = FALSE, ...)

### Arguments

`motifs` | See `convert_motifs()` for acceptable motif formats.
`use.type` | `character(1)` One of `c('PCM', 'PPM', 'PWM', 'ICM')`.
`method` | `character(1)` One of `c('PCC', 'MPCC', 'EUCL', 'MEUCL', 'SW', 'MSW', 'KL', 'MKL')`. See `compare_motifs()`.
`tryRC` | `logical(1)` Check if motif reverse complement leads to a better alignment. See `compare_motifs()`.
`min.overlap` | `numeric(1)` Minimum alignment overlap between motifs. If `min.overlap < 1`, this represents the minimum fraction between the two motifs during alignment. See `compare_motifs()`.
`min.mean.ic` | `numeric(1)` Minimum information content between the two motifs for an alignment to be scored. This helps prevent scoring alignments between low information content regions of two motifs. See `compare_motifs()`.
`relative_entropy` | `logical(1)` For ICM calculation. See `convert_type()`.
`normalise.scores` | `logical(1)` Favour alignments which leave fewer unaligned positions. See `compare_motifs()`.
`...` | Additional options for `ggseqlogo::geom_logo()`.

### Details

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.

### Value

A ggplot object.

### Author(s)

Benjamin Jean-Marie Tremblay, b2tremblay@uwaterloo.ca

### References

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.

### See Also

`compare_motifs()`, `add_multifreq()`

### Examples

    ## 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)

[Package universalmotif version 1.2.1 Index]