ggfortify | R Documentation |
Convert sequence data to a format suitable for logo plots
ggfortify(
data,
sequences,
treatment = NULL,
weight = NULL,
method = "shannon",
missing_encode = c(".")
)
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 '.'. |
data frame with position, element and information value
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")
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