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 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. |
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 non-sparse 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 gene-level differential connectivity p-value 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 p-values above 0.1.
plot(results[[1]], alpha = 0.1)
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