logo {DepLogo}

Sequence logo

Description

Plots 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

Details

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

Value

the vertical (y) offset after this plot

Author(s)

Jan Grau <[e-mail]>

Examples

# 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)