position_logo: Logo positioning for overlapping objects on top of one...
In gglogo: Geom for Logo Sequence Plots

position_classic is stacking objects in an ordered fashion from largest to smallest element, position_logo reverses the classic order and additionally shifts stacks downward to align the largest objects along their vertical minimum, position_fill additionally standardises each stack to have unit height.

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position_logo()

position_classic()

See geom_logo for more examples.

library(ggplot2)
data(sequences)

# to make the most of comparisons, largest letters ar aligned along their minimum to
# work out the main sequence.
ggplot(data = ggfortify(sequences, peptide, treatment = class)) +
  geom_logo(aes(x = class, y = bits, fill = Water, label = element), position="logo") + 
  facet_wrap(~position)

# in the classic logo plots letters are stacked in an ordered fasahion on top of each other
ggplot(data = ggfortify(sequences, peptide, treatment = class)) +
  geom_logo(aes(x = class, y = bits, fill = Water, label = element), position="classic") + 
  facet_wrap(~position)