DepLogo (version 1.0)

plotDeparcs: Plot a graph representation of dependency values.

Description

Plots a representation of dependency values as arcs between the sequence positions. Internally, dependency values are computed using getDeps on the data object.

Usage

plotDeparcs(data, axis.at.bottom = TRUE, add.legend = TRUE,
  show.pvals = FALSE, axis.labels = NULL, threshold = 0.1)

Arguments

data

the DLData object containing the data

axis.at.bottom

if TRUE, the x-axis is shown at the bottom (side=1) of the plot, and at the top (side=3) otherwise

add.legend

if TRUE a legend of the color scale is added to the plot

show.pvals

if TRUE, -log10 p-values (computed by pchisq) are shown instead of mutual information values

axis.labels

the labels of the x-axis

threshold

threshold in mutual information values, edges below this value are not shown; ignored in show.pvals=TRUE

Examples

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

# plot using default parameters
plotDeparcs(data)

# plot with axis at top, without a legend (color scale), and using p-values
plotDeparcs(data, axis.at.bottom = FALSE, add.legend = FALSE, show.pvals = TRUE)
# }