geom_logo: Sequence logo plots.

In heike/gglogo: Geom for Logo Sequence Plots

Sequence logo plots.

Description

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,
  ...
)

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.

Format

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

Examples

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")

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")

heike/gglogo documentation built on Feb. 3, 2024, 1:45 p.m.