ggfortify: Convert sequence data to a format suitable for logo plots

In gglogo: Geom for Logo Sequence Plots

Description

Convert sequence data to a format suitable for logo plots

Usage

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

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.

Value

data frame with position, element and information value

Examples

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")

gglogo documentation built on Jan. 29, 2020, 1:09 a.m.