gs_alluvial: Alluvial (sankey) plot for a set of genesets and the...

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

Alluvial (sankey) plot for a set of genesets and the associated genes

Description

Generate an interactive alluvial plot linking genesets to their associated genes

Usage

gs_alluvial(
  res_enrich,
  res_de,
  annotation_obj,
  gtl = NULL,
  n_gs = 5,
  gs_ids = NULL
)

gs_sankey(
  res_enrich,
  res_de,
  annotation_obj,
  gtl = NULL,
  n_gs = 5,
  gs_ids = 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 displayed
gs_ids	Character vector, containing a subset of gs_id as they are available in res_enrich. Lists the gene sets to be displayed.

Value

A plotly object

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)

gs_alluvial(
  res_enrich = res_enrich,
  res_de = res_de,
  annotation_obj = anno_df,
  n_gs = 4
)
# or using the alias...
gs_sankey(
  res_enrich = res_enrich,
  res_de = res_de,
  annotation_obj = anno_df,
  n_gs = 4
)

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