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]