dnapath (version 0.6.4)

plot.dnapath: Plot function for 'dnapath' object.

Description

Uses the plotting functions for networks from the SeqNet package seqnetdnapath

Usage

# S3 method for dnapath
plot(
  x,
  alpha = NULL,
  monotonized = FALSE,
  scale_edges = 1,
  scale_nodes = 1,
  ...
)

Arguments

x

A 'dnapath' object from dnapath.

alpha

Threshold for p-values to infer differentially connected edges. If NULL (the default) then no edges are removed from the plot.

monotonized

If TRUE, monotonized (i.e. step-down) p-values from the permutation test will be used.

scale_edges

(Optional) multiplier for edge widths.

scale_nodes

(Optional) multiplier for node radius

...

Additional arguments are passed into the plotting function plot_network.

Value

Plots the differential network and returns the graph object. See plot_network for details.

References

seqnetdnapath

Examples

# NOT RUN {
data(meso)
data(p53_pathways)
set.seed(0)
results <- dnapath(x = meso$gene_expression, pathway_list = p53_pathways,
                   groups = meso$groups, n_perm = 10)
# Plot of the differential network for pathway 1.
plot(results[[1]]) 
# Plot of the differential network for pathway 1; remove any edges from
# the plot that have p-values above 0.1.
plot(results[[1]], alpha = 0.1) 
# }