R: Plot function for 'dnapath' object.

plot.dnapath {dnapath} | R Documentation

## Plot function for 'dnapath' object.

### Description

Uses the plotting functions for networks from the `SeqNet` package (Grimes and Datta 2019)

### Usage

    ## S3 method for class 'dnapath'
    plot(
      x,
      alpha = NULL,
      monotonized = FALSE,
      only_dc = FALSE,
      require_dc_genes = 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.
`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 `plot_network`.

### Value

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

### References

Grimes T, Datta S (2019). SeqNet: Generate RNA-Seq Data from Gene-Gene Association Networks. R package version 1.1.0, https://CRAN.R-project.org/package=SeqNet.

### Examples

    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)

[Package dnapath version 0.7.4 Index]