Plot a motif from a MotifDB object

Plot a motif from a MotifDB object

Usage

# S4 method for class 'MotifDB'
plot(
  x,
  title = "",
  subtitle = ggplot2::waiver(),
  revcomp = FALSE,
  method = "bits",
  ...
)

Arguments

x

MotifDB object

title

title of the plot

subtitle

subtitle of the plot

revcomp

whether to plot the reverse complement of the PSSM

method

Height method, can be one of "bits" or "probability" (default:"bits")

...

Arguments passed on to ggseqlogo::ggseqlogo

data

Character vector of sequences or named list of sequences. All sequences must have same width

facet

Facet type, can be 'wrap' or 'grid'

scales

Facet scales, see facet_wrap

ncol

Number of columns, works only when facet='wrap', see facet_wrap

nrow

Number of rows, same as ncol

Value

a ggplot object

Examples

plot(MOTIF_DB["HOMER.GATA3_2"])

plot(MOTIF_DB["HNF1", pattern = T])

plot(MOTIF_DB[c("HOMER.GATA3_2", "JASPAR.CDX1")])