DepLogo (version 1.0)

logo: Sequence logo

Description

Plot a representation of a set of sequences as a sequence logo

Usage

logo(part, yoff, ic.scale = TRUE)

Arguments

part

the set of sequences as DLData object

yoff

the offset in y-direction within the current plot

ic.scale

if TRUE, symbols are scaled by "information content" of the distribution at each position

Value

the vertical (y) offset after this plot

Details

This function is a low-level plotting function (using polygon, internally).

Examples

# NOT RUN {
# read data and create DLData object
seqs <- read.table(system.file("extdata", "cjun.txt", package = "DepLogo"), 
    stringsAsFactors = FALSE)
data <- DLData(sequences = seqs[, 1], weights = log1p(seqs[,2]) )

# create high-level plot
plot(NULL, xlim = c(1, ncol(data$data) - 1), ylim = c(0, nrow(data$data)),  
   ylab = nrow(data$data), axes = FALSE)
# and add sequence logo and axis
logo(data, yoff = nrow(data$data))
axis(1)
# }