pathway_comparison_plot {hipathia} | R Documentation

## Plots pathway with colored significant paths

### Description

Plots the layout of a pathway, coloring the significant subpathways in different colors depending on whether they are significantly up- or down-regulated. Nodes may be also colored providing a suitable list of colors for each node. Function `node_color_per_de` assigns colors to the nodes depending on their differential expression.

### Usage

    pathway_comparison_plot(comp, metaginfo, pathway, conf = 0.05,
      node_colors = NULL, colors = "classic")

### Arguments

`comp` | Comparison data frame as returned by the `do_wilcox` function.
`metaginfo` | Pathways object.
`pathway` | Name of the pathway to be plotted.
`conf` | Level of significance of the comparison for the adjusted p-value. Default is 0.05.
`node_colors` | List, named by the pathway name, including the color of each node for each pathway.
`colors` | Either a character vector with 3 colors (indicating, in this order, down-regulation, non-significance and up-regulation colors) or a key name indicating the color scheme to be used. Options are:

### Value

Image in which a pathway is ploted. Edges are colored so that the UP- and DOWN-activated subpathways are identified.

### Slots

`classic`

  ColorBrewer blue, white and colorBrewer red.

`hipathia`

  Hipathia predefined color scheme: Green, white and orange. By default `classic` color scheme is applied.

### Examples

    data(comp)
    pathways <- load_pathways(species = "hsa", pathways_list = c("hsa03320",
    "hsa04012"))
    pathway_comparison_plot(comp, metaginfo = pathways, pathway = "hsa03320")

    ## Not run:
    data(results)
    data(brca)
    sample_group <- colData(brca)[,1]
    colors_de <- node_color_per_de(results, pathways,
    sample_group, "Tumor", "Normal")
    pathway_comparison_plot(comp, metaginfo = pathways, pathway = "hsa04012",
    node_colors = colors_de)

    ## End(Not run)

[Package hipathia version 1.0.0 Index]