Plot LOGO of pssm from dataset (e.g. "HOMER" or "JASPAR")

Usage

plot_pssm_logo_dataset(
  motif,
  dataset = all_motif_datasets(),
  title = motif,
  subtitle = ggplot2::waiver(),
  pos_bits_thresh = NULL,
  revcomp = FALSE,
  method = "bits"
)

Arguments

motif: the motif name (e.g. "GATA4")
dataset: a data frame with PSSMs ('A', 'C', 'G' and 'T' columns), with an additional column 'motif' containing the motif name, for example HOMER_motifs, JASPAR_motifs or all_motif_datasets()
title: title of the plot
subtitle: subtitle of the plot
pos_bits_thresh: Positions with bits above this threshold would be highlighted in red. If NULL, no positions would be highlighted.
revcomp: whether to plot the reverse complement of the PSSM
method: Height method, can be one of "bits" or "probability" (default:"bits")

Value

a ggplot object

Examples


plot_pssm_logo_dataset("JASPAR.Brachyury")


plot_pssm_logo_dataset("GATA5", JASPAR_motifs)