seqLogo: Plot a sequence logo for a given position weight matrix

In thephilross/seqLogo: Sequence logos for DNA sequence alignments

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.

Author(s)

Oliver Bembom, [e-mail]

Examples

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

thephilross/seqLogo documentation built on May 31, 2019, 9:50 a.m.