view_logo: Plot logos from numeric matrices.

In bjmt/universalmotif: Import, Modify, and Export Motifs with R

Plot logos from numeric matrices.

Description

This function provides the plotting capabilities of view_motifs() without requiring universalmotif-class objects. Instead, it takes a numeric matrix with row names as input. Additionally, columns can be of any height and letters can be a mix of different character lengths.

Usage

view_logo(x, fontDF = NULL, fill = "black", colour.scheme = NULL,
  min.height = 0.01, x.spacer = 0.04, y.spacer = 0.01,
  sort.positions = FALSE, sort.positions.decreasing = TRUE,
  fit.to.height = NULL)

Arguments

x	A numeric matrix with row names. The row names can be a mix of different character lengths.
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.
fill	character A single colour to fill all letters with. Ignored if colour.scheme is provided.
colour.scheme	character A named character vector of colour names. Provide colours for individual letters, even if the row names are made up of multiple characters.
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 letters made up of multiple characters.
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.
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").

Value

A ggplot object. If you wish to plot the data yourself from polygon paths, access them using ⁠$data⁠ on the output object. The theme theme_void() is applied to the object; apply your own theme or adjust specific plot parameters with theme() to change this.

Author(s)

Benjamin Jean-Marie Tremblay, [e-mail]

See Also

view_motifs()

Examples

## Feel free to mix and match row name character lengths and column sums.
data(examplemotif)
toplot <- examplemotif["motif"]
toplot[4] <- 2
toplot[20] <- -0.5
rownames(toplot)[1] <- "AA"
view_logo(toplot)

bjmt/universalmotif documentation built on Nov. 16, 2024, 7:38 a.m.