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, fontsize=12)

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.

fontsize

font size of the template for grImport, default 12. Higher value make better quality figure, but also increase the file size.

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 1.26.0 Index]