enhance_table: Visually enhances a functional enrichment result table

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

Description

Creates a visual summary for the results of a functional enrichment analysis, by displaying also the components of each gene set and their expression change in the contrast of interest

Usage

enhance_table(
  res_enrich,
  res_de,
  annotation_obj,
  n_gs = 50,
  gs_ids = NULL,
  chars_limit = 70,
  plot_title = 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.
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.
chars_limit	Integer, number of characters to be displayed for each geneset name.
plot_title	Character string, used as title for the plot. If left NULL, it defaults to a general description of the plot and of the DE contrast

Value

A ggplot 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)
enhance_table(res_enrich,
              res_de,
              anno_df,
              n_gs = 10)

GeneTonic documentation built on Nov. 8, 2020, 5:27 p.m.