ggs_graph: Construct a gene-geneset-graph

In federicomarini/GeneTonic: Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis

Construct a gene-geneset-graph

Description

Construct a gene-geneset-graph from the results of a functional enrichment analysis

Usage

ggs_graph(
  res_enrich,
  res_de,
  annotation_obj = NULL,
  gtl = NULL,
  n_gs = 15,
  gs_ids = NULL,
  prettify = TRUE,
  geneset_graph_color = "gold",
  genes_graph_colpal = NULL
)

Arguments

res_enrich	A data.frame object, storing the result of the functional enrichment analysis. See more in the main function, GeneTonic(), to check the formatting requirements (a minimal set of columns should be present).
res_de	A DESeqResults object.
annotation_obj	A data.frame object with the feature annotation information, with at least two columns, gene_id and gene_name.
gtl	A GeneTonic-list object, containing in its slots the arguments specified above: dds, res_de, res_enrich, and annotation_obj - the names of the list must be specified following the content they are expecting
n_gs	Integer value, corresponding to the maximal number of gene sets to be included
gs_ids	Character vector, containing a subset of gs_id as they are available in res_enrich. Lists the gene sets to be included in addition to the top ones (via n_gs)
prettify	Logical, controlling the aspect of the returned graph object. If TRUE (default value), different shapes of the nodes are returned, based on the node type
geneset_graph_color	Character value, specifying which color should be used for the fill of the shapes related to the gene sets.
genes_graph_colpal	A vector of colors, also provided with their hex string, to be used as a palette for coloring the gene nodes. If unspecified, defaults to a color ramp palette interpolating from blue through yellow to red.

Value

An igraph object to be further manipulated or processed/plotted (e.g. via igraph::plot.igraph() or visNetwork::visIgraph())

Examples

library("macrophage")
library("DESeq2")
library("org.Hs.eg.db")
library("AnnotationDbi")

# dds object
data("gse", package = "macrophage")
dds_macrophage <- DESeqDataSet(gse, design = ~ line + condition)
rownames(dds_macrophage) <- substr(rownames(dds_macrophage), 1, 15)
dds_macrophage <- estimateSizeFactors(dds_macrophage)

# annotation object
anno_df <- data.frame(
  gene_id = rownames(dds_macrophage),
  gene_name = mapIds(org.Hs.eg.db,
    keys = rownames(dds_macrophage),
    column = "SYMBOL",
    keytype = "ENSEMBL"
  ),
  stringsAsFactors = FALSE,
  row.names = rownames(dds_macrophage)
)

# res object
data(res_de_macrophage, package = "GeneTonic")
res_de <- res_macrophage_IFNg_vs_naive

# res_enrich object
data(res_enrich_macrophage, package = "GeneTonic")
res_enrich <- shake_topGOtableResult(topgoDE_macrophage_IFNg_vs_naive)
res_enrich <- get_aggrscores(res_enrich, res_de, anno_df)

ggs <- ggs_graph(
  res_enrich,
  res_de,
  anno_df
)

ggs

#' # could be viewed interactively with
# library(visNetwork)
# library(magrittr)
# ggs %>%
#   visIgraph() %>%
#   visOptions(highlightNearest = list(enabled = TRUE,
#                                      degree = 1,
#                                      hover = TRUE),
#             nodesIdSelection = TRUE)

federicomarini/GeneTonic documentation built on Dec. 21, 2024, 10:05 p.m.