plotAffinityLogo {motifStack} | R Documentation

## plot affinity logo

### Description

plot affinity logo

### Usage

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

### Arguments

`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

### 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 1.36.1 Index]