plotAffinityLogo {motifStack} | R Documentation |
plot affinity logo
plotAffinityLogo(psam, motifName, font="Helvetica-Bold", colset=c("#00811B","#2000C7","#FFB32C","#D00001"), alpha=0.5, newpage=TRUE, fontsize=12)
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. |
none
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
psam <- importMatrix(file.path(find.package("motifStack"), "extdata", "PSAM.mxr"), format="psam")[[1]] plotAffinityLogo(psam)