MotIV (version 1.28.0)

seqLogo2: 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

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.

Value

None.

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.

Examples

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