seqLogo2: Plot a sequence logo for a given position weight matrix

In alyst/MotIV: Motif Identification and Validation

Description

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

Usage

  seqLogo2(pwm, ic.scale=TRUE, xaxis=TRUE, yaxis=TRUE, xfontsize=15, yfontsize=15,vmargins=c(0,0),hmargins=c(0,0),size=1, trim=0)

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.
vmargins	numeric Vertical margins.
hmargins	numeric Horizontal margins.
size	numeric Graphic size.
trim	numeric Print nucleotide only if the infomation content is superior to this trim threshold.

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.

This is an internal function for the package MotIV. User should prefer the seqLogo function from the package seqLogo to visualize individual motif.

Value

None.

Author(s)

Oliver Bembom, [e-mail], modified by Eloi Mercier <[e-mail]>

Examples

#mFile <- system.file("Exfiles/pwm1", package="seqLogo")
#m <- read.table(mFile)
#pwm <- makePWM(m)
#seqLogo2(pwm)

alyst/MotIV documentation built on May 12, 2019, 2:33 a.m.