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

In ivanek/seqLogo: Sequence logos for DNA sequence alignments

Plot a sequence logo for a given position weight matrix

Description

This function takes the alphabet*width position weight matrix of a sequence motif and plots the corresponding sequence logo.

Usage

seqLogo(pwm, ic.scale=TRUE, xaxis=TRUE, yaxis=TRUE, xfontsize=15, yfontsize=15,
        fill=c(A='#61D04F', C='#2297E6', G='#F5C710', T='#DF536B'))

Arguments

pwm	numeric. The alphabet*width 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.
fill	character. Fill color to be used for the letters. Must be a named character vector of length equal to number of rows in pwm slot and names identical to its rownames.

Value

NULL.

Author(s)

Oliver Bembom

Examples

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

ivanek/seqLogo documentation built on May 4, 2023, 12:39 p.m.