Convert sequence data to a format suitable for logo plots

Usage

ggfortify(
  data,
  sequences,
  treatment = NULL,
  weight = NULL,
  method = "shannon",
  missing_encode = c(".")
)

Arguments

data: data frame with the sequences
sequences: variable containing the sequences
treatment: co-variate(s) used in collecting sequence data
weight: numeric variable of weights
method: either "shannon" or "frequency" for Shannon information or relative frequency of element by position.
missing_encode: which character value(s) signifies a missing element in a sequence? defaults to `.`.

Value

data frame with position, element and information value

Examples

# \donttest{
library(ggplot2)
data(sequences)

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


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

# }