node_color_per_de: Colors of the nodes by its differential expression

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

Colors of the nodes by its differential expression

Description

Performs a Limma differential expression on the nodes and computes the colors of the nodes depending on it_ 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_per_de(
  results,
  metaginfo,
  group,
  expdes,
  g2 = NULL,
  group_by = "pathway",
  colors = "classic",
  conf = 0.05,
  adjust = TRUE
)

Arguments

results	Object of results as provided by the hipathia function_
metaginfo	Object of pathways_
group	Character indicating the column in which the group variable is stored, in case the object provided to hipathia was a SummarizedExperiment, or a vector with the class to which each sample belongs. Samples must be ordered as in results.
expdes	String, either the comparison to be performed or the label of the first group to be compared.
g2	String, label of the second group to be compared. Only necessary in case expdes is the name of the first group, not the comparison.
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)
colors_de <- node_color_per_de(results, pathways, "group", "Tumor - Normal")
colors_de <- node_color_per_de(results, pathways, "group", "Tumor", "Normal")

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