plot.dnapath  R Documentation 
Uses the plotting functions for networks from the SeqNet
package
\insertCiteseqnetdnapath
## S3 method for class 'dnapath' plot( x, alpha = NULL, monotonized = FALSE, only_dc = FALSE, require_dc_genes = FALSE, scale_edges = 1, scale_nodes = 1, ... )
x 
A 'dnapath' object from 
alpha 
Threshold for pvalues to infer differentially connected edges. If NULL (the default) then no edges are removed from the plot. 
monotonized 
If TRUE, monotonized (i.e. stepdown) pvalues from the permutation test will be used. 
only_dc 
If TRUE, only differentially connected edges will be shown; any edges that are present in both groups are hidden. If FALSE, the edges shared by both groups are shown. If a nonsparse estimator for network edges is used, then the graph may be dense and setting this argument to TRUE will be useful for highlighting the DC edges. 
require_dc_genes 
If TRUE, the genelevel differential connectivity pvalue of the two genes for a given edge are also considered when deciding whether an edge is differentially connected. If neither gene is significantly differentially connected, then the edge between them will not be either. 
scale_edges 
(Optional) multiplier for edge widths. 
scale_nodes 
(Optional) multiplier for node radius 
... 
Additional arguments are passed into the plotting function

Plots the differential network and returns the graph object.
See plot_network
for details.
seqnetdnapath
data(meso) data(p53_pathways) set.seed(0) results < dnapath(x = meso$gene_expression, pathway_list = p53_pathways, group_labels = meso$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 pvalues above 0.1. plot(results[[1]], alpha = 0.1)
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