view_motifs: Plot motif logos.
In bjmt/universalmotif: Import, Modify, and Export Motifs with R

view_motifs

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 = "ALLR", tryRC = TRUE,
  min.overlap = 6, min.mean.ic = 0.25, relative_entropy = FALSE,
  normalise.scores = FALSE, min.position.ic = 0, score.strat = "sum",
  return.raw = FALSE, dedup.names = TRUE, show.positions = TRUE,
  show.positions.once = TRUE, show.names = TRUE, names.pos = c("top",
  "right"), use.freq = 1, colour.scheme = NULL, fontDF = NULL,
  min.height = 0.01, x.spacer = if (use.freq == 1) 0.04 else 0.1,
  y.spacer = 0.01, sort.positions = !use.type %in% c("PCM", "PPM"),
  sort.positions.decreasing = TRUE, text.size = 16, fit.to.height = if
  (use.type == "PPM") 1 else NULL, RC.text = " [RC]", ...)

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 PCC, EUCL, SW, KL, ALLR, BHAT, HELL, SEUCL, MAN, ALLR_LL, WEUCL, WPCC. See details.
`tryRC`	`logical(1)` Try the reverse complement of the motifs as well, report the best score.
`min.overlap`	`numeric(1)` Minimum overlap required when aligning the motifs. Setting this to a number higher then the width of the motifs will not allow any overhangs. Can also be a number between 0 and 1, representing the minimum fraction that the motifs must overlap.
`min.mean.ic`	`numeric(1)` Minimum mean 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. Note that this can result in some comparisons failing if no alignment passes the mean IC threshold. Use `average_ic()` to filter out low IC motifs to get around this if you want to avoid getting `NA`s in your output.
`relative_entropy`	`logical(1)` Change the ICM calculation affecting `min.position.ic` and `min.mean.ic`. See `convert_type()`.
`normalise.scores`	`logical(1)` Favour alignments which leave fewer unaligned positions, as well as alignments between motifs of similar length. Similarity scores are multiplied by the ratio of aligned positions to the total number of positions in the larger motif, and the inverse for distance scores.
`min.position.ic`	`numeric(1)` Minimum information content required between individual alignment positions for it to be counted in the final alignment score. It is recommended to use this together with `normalise.scores = TRUE`, as this will help punish scores resulting from only a fraction of an alignment.
`score.strat`	`character(1)` How to handle column scores calculated from motif alignments. "sum": add up all scores. "a.mean": take the arithmetic mean. "g.mean": take the geometric mean. "median": take the median. "wa.mean", "wg.mean": weighted arithmetic/geometric mean. "fzt": Fisher Z-transform. Weights are the total information content shared between aligned columns.
`return.raw`	`logical(1)` Instead of returning a plot, return the aligned named matrices used to generate the plot. This can be useful if you wish to use `view_motifs()` alignment capabilities for custom plotting uses. Alignment is performed by adding empty columns to the left or right of motifs to generate matrices of equal length.
`dedup.names`	`logical(1)` Plotting motifs with duplicated names is not allowed. Setting this to `TRUE` allows the names to be modified for plotting.
`show.positions`	`logical(1)` Show x-axis position tick labels.
`show.positions.once`	`logical(1)` When plotting multiple motifs, show x-axis position tick labels only once. If `FALSE`, then x-axis tick labels are specific to each motif.
`show.names`	`logical(1)` Add motif names when plotting multiple motifs.
`names.pos`	`character(1)` Motif name locations. Either above (`top`) or to the right (`right`) of the logos.
`use.freq`	`numeric(1)` Plot higher order motifs from the `multifreq` slot.
`colour.scheme`	`character` A named character vector of colour names. Default colours are provided for DNA, RNA, and AA motifs if left `NULL`.
`fontDF`	`data.frame` or `DataFrame` Polygon data for letters used for plotting, as generated by the `createPolygons()` function from the `gglogo` package. See the `fontDFroboto` data object (which is used by default when `fontDF = NULL`). See `Examples` for how to generate your own font set. Expected columns: `x`, `y`, `order`, `group`; additional columns will be ignored.
`min.height`	`numeric(1)` Minimum height for a letter to be plotted. The number is taken as the fraction of the total height of the plot. The default value is to not show letters which take up 1% or less of the vertical space. For smaller figures it is recommended to increase this value, and vice versa for larger figures.
`x.spacer`	`numeric(1)` Add horizontal spacing between letters. The number is taken as the fraction of the width of an individual position. Increasing this value is recommended for plotting multifreq motifs.
`y.spacer`	`numeric(1)` Add vertical spacing between letters. The number is taken as the fraction nof the total height of the plot.
`sort.positions`	`logical(1)` Sort letters vertically per position by height.
`sort.positions.decreasing`	`logical(1)` Sort in decreasing or increasing order based on letter height.
`text.size`	`numeric(1)` Text size for labels.
`fit.to.height`	`numeric(1)` Normalize the per position height to this value. If `NULL`, no normalization is applied. Note that this parameter is ignored if `use.type = c("PWM", "ICM")`.
`RC.text`	`character(1)` The text to display alongside the name of motifs shown as their reverse complement.
`...`	Unused. Was previously in place to allow extra args to be given to `ggseqlogo::ggseqlogo`, however `universalmotif` now implements its own motif plotting code directly with `ggplot2`.

Details

See compare_motifs() for more info on comparison parameters.

See view_logo() to plot from a numeric matrix with arbitrary values instead of a motif object.

Note: score.strat = "a.mean" is NOT recommended, as view_motifs() will not discriminate between two alignments with equal mean scores, even if one alignment is longer than the other.

Note: if you want to plot the motifs yourself, you can set return.raw=TRUE to get the numeric motif matrices and calculate the polygon paths on your own or access the polygon path data directly from the final ggplot object using ⁠$data⁠.

Value

A ggplot object. If return.raw = TRUE, a list of matrices.

Author(s)

Benjamin Jean-Marie Tremblay, benjamin.tremblay@uwaterloo.ca

Examples

## Plotting multifreq motifs:
data(examplemotif2)
view_motifs(examplemotif2, use.freq = 2)

## Generate your own letter set:
## Not run: 

library(gglogo)  # install from CRAN first if needed
fontDFtimes <- createPolygons(LETTERS, "Times", 800, scale = TRUE)
view_motifs(examplemotif2, fontDF = fontDFtimes)

## Note: setting `scale = TRUE` is necessary to properly align letters
## vertically, but this has the effect of horizontally stretching out
## letters which shouldn't be stretched (such as "I"). If you need to plot
## letters which have been badly horizontally scaled, you can fix them
## manually as demonstrated here:

# Retrieve the x-coordinates for the desired letter:
tofix <- fontDFtimes$x[fontDFtimes$group == "I"]
# Scale the letter x-coordinates:
tofix <- tofix * 0.35
# Remember to center the letter around 0.5 again:
tofix <- tofix + (1 - max(tofix)) / 2
# Apply the fix:
fontDFtimes$x[fontDFtimes$group == "I"] <- tofix
view_motifs(create_motif("AIG", alphabet = "AA"), fontDF = fontDFtimes)


## End(Not run)

bjmt/universalmotif documentation built on March 18, 2024, 8:32 a.m.