Plot a sequence logo for a given position weight matrix

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Description

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

Usage

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  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, bembom@berkeley.edu

Examples

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

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