seqLogo: seqLogo

In markheron/pRon: pretty Representations of oligo-nucleotides

Description

Plot a PWM sequence logo.

Usage

seqLogo(pwm, background = c(A = 0.25, C = 0.25, G = 0.25, T = 0.25),
  ytype = "information", xaxis = TRUE, xlim = c(0, ncol(pwm)),
  yaxis = TRUE, ylim = NULL, xlab = "Position", xfontsize = 15,
  yfontsize = 15, region = c(0, 0, 1, 1), ...)

Arguments

pwm	position weight matrix to create a Sequence Logo from
background	(numeric vector-4) background probabilities of the nucleotides for information gain computation default all=0.25
ytype	(character) the type of y-axis to be used "information" (or "ic", "content") for information content (default); "relative" (or "gain") for information gain; "probabilities" (or anything else) for probabilities
xaxis	(logical) should an x-axis be drawn or vector of labels for the xaxis (must be same length as pwm)
xlim	(numeric vector-2) default c(0,ncol(pwm)) see graphical parameters
yaxis	(logical) should an y-axis be drawn
ylim	(numeric vector-2) default NULL see graphical parameters
xlab	(character) see graphical parameters
xfontsize	(integer) size for x-axis text
yfontsize	(integer) size for y-axis text
region	in which to plot the figure, set by four margin values, set to par("mar") for default full plot
...	further parameters to be passed through to dataViewport

Examples

pwm <- rbind( A=c( 0,  0, 15,  5,  5,  1, 0.1),
              C=c(10,  0,  0,  5,  5,  2, 0.1),
              G=c(10,  0,  5,  0,  5,  3, 0.1),
              T=c( 0, 20,  0, 10,  5, 14,19.7)) /20
              
seqLogo(pwm, region=par("mar"))

markheron/pRon documentation built on Feb. 18, 2020, 12:33 a.m.