pathway_comparison_plot: Plots pathway with colored significant paths

In martahidalgo/hipathia: HiPathia: High-throughput Pathway Analysis

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

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

## End(Not run)

martahidalgo/hipathia documentation built on Jan. 12, 2023, 1:44 p.m.