plotMotifLogo {motifStack} | R Documentation

## plot sequence logo

### Description

plot amino acid or DNA sequence logo

### Usage

    plotMotifLogo(
      pfm,
      motifName,
      p = rep(0.25, 4),
      font = "Helvetica-Bold",
      fontface = "bold",
      colset = c("#00811B", "#2000C7", "#FFB32C", "#D00001"),
      xaxis = TRUE,
      yaxis = TRUE,
      xlab = "position",
      ylab = "bits",
      xlcex = 1.2,
      ylcex = 1.2,
      ncex = 1.2,
      ic.scale = TRUE,
      newpage = TRUE,
      margins = c(4.1, 4.1, 2.1, 0.1),
      draw = TRUE
    )

### Arguments

`pfm` | a position frequency matrices
`motifName` | motif name
`p` | background possibility
`font` | font of logo
`fontface` | fontface of logo
`colset` | color setting for each logo letter
`xaxis` | draw x-axis or not
`yaxis` | draw y-axis or not
`xlab` | x-label, do nothing if set xlab as NA
`ylab` | y-label, do nothing if set ylab as NA
`xlcex` | cex value for x-label
`ylcex` | cex value for y-label
`ncex` | cex value for motif name
`ic.scale` | logical If TRUE, the height of each column is proportional to its information content. Otherwise, all columns have the same height.
`newpage` | logical If TRUE, plot it in a new page.
`margins` | A numeric vector interpreted in the same way as par(mar) in base graphics.
`draw` | Vector (logical(1)). TRUE to plot. FALSE, return a gList

### Value

none

### Examples

    pcm<-matrix(runif(40,0,100),nrow=4,ncol=10)
    pfm<-pcm2pfm(pcm)
    rownames(pfm)<-c("A","C","G","T")
    plotMotifLogo(pfm)

[Package motifStack version 1.36.1 Index]