plotAffinityLogo: plot affinity logo

In jianhong/motifStack: Plot stacked logos for single or multiple DNA, RNA and amino acid sequence

plot affinity logo

Description

plot affinity logo

Usage

plotAffinityLogo(
  psam,
  motifName,
  font = "sans",
  fontface = "bold",
  colset = c("#00811B", "#2000C7", "#FFB32C", "#D00001"),
  alpha = 0.5,
  newpage = TRUE,
  draw = TRUE
)

Arguments

psam	a position-specific affinity matrix
motifName	motif name
font	font of logo
fontface	fontface of logo
colset	color setting for each logo letter
alpha	Alpha channel for transparency of low affinity letters.
newpage	plot in a new canvas or not.
draw	Vector (logical(1)). TRUE to plot. FALSE, return a gList

Value

none

References

Barrett C. Foat, Alexandre V. Morozov, Harmen J. Bussemaker; Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE, Bioinformatics, Volume 22, Issue 14, 15 July 2006, Pages e141-e149, https://doi.org/10.1093/bioinformatics/btl223

Examples

psam <- importMatrix(file.path(find.package("motifStack"), "extdata", "PSAM.mxr"), 
                     format="psam")[[1]]
plotAffinityLogo(psam)

jianhong/motifStack documentation built on Nov. 5, 2024, 7:47 a.m.