plotDepmatrix {DepLogo}

Plots a matrix representation of dependency values

Description

Plots a representation of dependency values as a triangular matrix rotated by 45 degrees. Internally, dependency values are computed using getDeps on the data object.

Usage

plotDepmatrix(
  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

ignored

Author(s)

Jan Grau <[e-mail]>

Examples

# 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
plotDepmatrix(data)

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