plot_corecmotif: Plot CoRecMotifs and their matching reference motifs

In Siggers-Lab/hTF_array: Process and Visualize CoRec Data

Plot CoRecMotifs and their matching reference motifs

Description

Creates a motif logo plot of a CoRecMotif and/or its matching reference motif. There are several types of logos to choose from.

Usage

plot_corecmotif(
  corecmotif,
  corecmotif_logo_type = c("delta_zscore", "ICM", "PWM", "PPM", "none"),
  reference_logo_type = c("ICM", "PWM", "PPM", "none"),
  reverse_complement = FALSE,
  correct_orientation = TRUE,
  fade_corecmotif = FALSE,
  fade_reference = FALSE,
  check_corecmotif = TRUE
)

Arguments

corecmotif	CoRecMotif. The CoRecMotif to plot.
corecmotif_logo_type	character(1). One of "delta_zscore", "ICM", "PWM", "PPM", or "none". The type of logo to plot for the CoRecMotif. (Default: "delta_zscore")
reference_logo_type	character(1). One of "ICM", "PWM", "PPM", or "none". The type of logo to plot for the matching reference motif. (Default: "ICM")
reverse_complement	logical(1). Should the CoRecMotif be reversed? (Default: False)
correct_orientation	logical(1). Should the reference motif be reversed if necessary to match the CoRecMotif's orientation? (Default: TRUE)
fade_corecmotif	logical(1). Should the CoRecMotif logo be faded? (Default: FALSE)
fade_reference	logical(1). Should the reference motif logo be faded? (Default: FALSE)
check_corecmotif	logical(1). Should corecmotif be checked for validity? Setting this to FALSE can increase speed, but if corecmotif is not a valid CoRecMotif, it may produce uninformative error messages. (Default: TRUE)

Value

A ggplot object.

Examples

print("FILL THIS IN")

Siggers-Lab/hTF_array documentation built on Feb. 7, 2024, 11:25 p.m.