plotAffinityLogo {motifStack}R Documentation

plot affinity logo

Description

plot affinity logo

Usage

plotAffinityLogo(psam, motifName, font="Helvetica-Bold",
                             colset=c("#00811B","#2000C7","#FFB32C","#D00001"),
                             alpha=0.5, newpage=TRUE)

Arguments

psam

a position-specific affinity matrix

motifName

motif name

font

font 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.

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)

[Package motifStack version 1.28.0 Index]