plotDeparcs: Plots a graph representation of dependency values
In Jstacs/DepLogo: Dependency Logo

Description Usage Arguments Author(s) Examples

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

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

`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`

Jan Grau <grau@informatik.uni-halle.de>

# 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)