gglogo-alphabet.R
In gglogo: Geom for Logo Sequence Plots

## ----setup, echo=FALSE--------------------------------------------------------
knitr::opts_chunk$set(fig.width = 6,
                      fig.height = 4,
                      fig.align='center',
                      dev = "png")

## ---- message=FALSE-----------------------------------------------------------
library(ggplot2)
library(gglogo)
data(alphabet)
head(alphabet)

## -----------------------------------------------------------------------------
ggplot(data = alphabet, aes(x = x, y = y)) +
  geom_polygon() +
  facet_wrap(~group, ncol = 13) +
  coord_equal()

## ---- warning=FALSE-----------------------------------------------------------
alphas <- c(LETTERS, letters, 0:9)
alphabet_garamond <- createPolygons(alphas, font="Garamond")
alphabet_garamond$group <- factor(alphabet_garamond$group, levels=alphas)

ggplot(alphabet_garamond, aes(x = x, y = y, group = group)) +
  geom_polygon(aes(subgroup=pathGroup)) +
  facet_wrap(~group, ncol = 13)

## ---- warning=FALSE-----------------------------------------------------------
alphas <- c(LETTERS, letters, 0:9)
alphabet_helvetica <- createPolygons(alphas, font="Helvetica")
alphabet_helvetica$group <- factor(alphabet_helvetica$group, levels=alphas)

ggplot(alphabet_helvetica, aes(x = x, y = y)) +
  geom_polygon() +
  facet_wrap(~group, ncol = 13)

## ---- warning=FALSE-----------------------------------------------------------
alphas <- c(LETTERS, letters, 0:9)
alphabet_comic <- createPolygons(alphas, font="Comic Sans MS", scale=TRUE)
alphabet_comic$group <- factor(alphabet_comic$group, levels=alphas)

ggplot(alphabet_comic, aes(x = x, y = y)) +
  geom_polygon() +
  facet_wrap(~group, ncol = 13)

## -----------------------------------------------------------------------------
data(sequences)
ggplot(data = ggfortify(sequences, peptide, treatment = class)) +
  geom_logo( aes(x = class, y = bits, label=element, group=element, 
                fill = interaction(Polarity, Water)), 
            alphabet = alphabet_braille, 
            alpha = 0.8) +
  facet_wrap(~position) +
  scale_fill_brewer(palette="Paired")