seqLogo {seqLogo}R Documentation

Plot a sequence logo for a given position weight matrix

Description

This function takes the 4xW position weight matrix of a DNA sequence motif and plots the corresponding sequence logo.

Usage

  seqLogo(pwm, ic.scale=TRUE, xaxis=TRUE, yaxis=TRUE, xfontsize=15, yfontsize=15)

Arguments

pwm numeric The 4xW position weight matrix.
ic.scale logical If TRUE, the height of each column is proportional to its information content. Otherwise, all columns have the same height.
xaxis logical If TRUE, an X-axis will be plotted.
yaxis logical If TRUE, a Y-axis will be plotted.
xfontsize numeric Font size to be used for the X-axis.
yfontsize numeric Font size to be used for the Y-axis.

Details

Within each column, the height of a given letter is proportional to its frequency at that position. If ic.scale is TRUE, the height of each column in the plot indicates the information content at that position of the motif. Otherwise, the height of all columns are identical.

Value

None.

Note

Author(s)

Oliver Bembom, bembom@berkeley.edu

References

See Also

Examples

mFile <- system.file("Exfiles/pwm1", package="seqLogo")
m <- read.table(mFile)
pwm <- makePWM(m)
seqLogo(pwm)

[Package seqLogo version 1.4.0 Index]