Sequence logo plots.

Usage

GeomLogo

geom_logo(
  mapping = NULL,
  data = NULL,
  stat = "logo",
  position = "logo",
  show.legend = NA,
  inherit.aes = TRUE,
  width = 0.9,
  alpha = 0.6,
  na.rm = TRUE,
  alphabet = NULL,
  ...
)

Format

An object of class GeomLogo (inherits from Geom, ggproto, gg) of length 6.

Arguments

mapping: The aesthetic mapping, usually constructed with aes or aes_string. Only needs to be set at the layer level if you are overriding the plot defaults.
data: A layer specific dataset - only needed if you want to override the plot defaults,
stat: The statistical transformation to use on the data for this layer,
position: The position adjustment to use for overlappling points on this layer,
show.legend: Whether to show the legend or not
inherit.aes: Whether to inherit the aes or not
width: maximum width of the letters, defaults to 0.9,
alpha: amount of alpha blending used for putting letters on top of rectangle, defaults to 0.25,
na.rm: Whether to remove NAs or not
alphabet: Specifies which alphabet is used in rendering the logo. alphabet can be a dataframe (output from createPolygons), a character specifying a font or NULL. If NULL, the default alphabet set is used (based on Helvetica). Use output from `createPolygons` to generate alphabet polygons for a different font.
...: other arguments passed on to layer. This can include aesthetics whose values you want to set, not map. See layer for more details.

Examples

# \donttest{
library(ggplot2)
data(sequences)
ggplot(data = ggfortify(sequences, peptide)) +
  geom_logo(aes(x=position, y=bits, group=element,
     label=element, fill=interaction(Polarity, Water)),
     alpha = 0.6)  +
  scale_fill_brewer(palette="Paired") +
  theme(legend.position = "bottom")
#> Warning: Using the `size` aesthetic with geom_rect was deprecated in ggplot2 3.4.0.
#> ℹ Please use the `linewidth` aesthetic instead.
#> Warning: Using the `size` aesthetic with geom_polygon was deprecated in ggplot2 3.4.0.
#> ℹ Please use the `linewidth` aesthetic instead.


ggplot(data = ggfortify(sequences, peptide, treatment = class)) +
  geom_logo(aes(x=class, y=bits, group=element,
     label=element, fill=element)) +
  facet_wrap(~position, ncol=18) +
  theme(legend.position = "bottom")


ggplot(data = ggfortify(sequences, peptide, treatment = class)) +
  geom_logo(aes(x=position, y=bits, group=element, label=element, fill=element)) +
  facet_wrap(~class, ncol=1) + theme_bw()


ggplot(data = ggfortify(sequences, peptide, treatment = class)) +
  geom_logo(aes(x=class, y=bits, group=element,
                label=element, fill=interaction(Polarity, Water))) +
  scale_fill_brewer("Amino-acids properties", palette="Paired") +
  facet_wrap(~position, ncol=18) +
  theme(legend.position="bottom") +
  xlab("") + ylab("Shannon information in bits")


# }