plotAffinityLogo {motifStack} | R Documentation |
plot affinity logo
plotAffinityLogo( psam, motifName, font = "Helvetica-Bold", fontface = "bold", colset = c("#00811B", "#2000C7", "#FFB32C", "#D00001"), alpha = 0.5, newpage = TRUE, draw = TRUE )
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 |
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)