node_color: Get colors of the nodes from a comparison file

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

Get colors of the nodes from a comparison file

Description

Computes the colors of the nodes depending on the sign and p.value from the provided file. Significant up- and down-regulated nodes are depicted with the selected color, with a gradient towards the non-significant color depending on the value of the p-value. Smaller p-values give rise to purer colors than higher p-values.

Usage

node_color(
  comp,
  metaginfo,
  group_by = "pathway",
  colors = "classic",
  conf = 0.05,
  adjust = TRUE
)

Arguments

comp	Comparison file as returned by do_wilcoxon. Must include a column named "UP/DOWN" with the sign of the comparison coded as UP or DOWN, a column named "p.value" of raw p.values and a column named "FDRp.value" of adjusted p.values.
metaginfo	Object of pathways.
group_by	How to group the subpathways to be visualized. By default they are grouped by the pathway to which they belong. Available groupings include "uniprot", to group subpathways by their annotated Uniprot functions, "GO", to group subpathways by their annotated GO terms, and "genes", to group subpathways by the genes they include. Default is set to "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:
conf	Level of significance of the comparison for the adjusted p-value.
adjust	Boolean, whether to adjust the p.value from the comparison. Default is TRUE.

Value

List of color vectors, named by the pathways to which they belong. The color vectors represent the differential expression of the nodes in each pathway.

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(results)
data(brca)
pathways_list <- c("hsa03320", "hsa04012")
pathways <- load_pathways(species = "hsa", pathways_list)
comp <- do_wilcoxon(results[["nodes"]], "group", "Tumor", "Normal")
colors_de <- node_color(comp, pathways)

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