gs_summary_overview: Plots a summary of enrichment results

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

Plots a summary of enrichment results

Description

Plots a summary of enrichment results for one set

Usage

gs_summary_overview(
  res_enrich,
  gtl = NULL,
  n_gs = 20,
  p_value_column = "gs_pvalue",
  color_by = "z_score",
  return_barchart = FALSE
)

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).
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
p_value_column	Character string, specifying the column of res_enrich where the p-value to be represented is specified. Defaults to gs_pvalue (it could have other values, in case more than one p-value - or an adjusted p-value - have been specified).
color_by	Character, specifying the column of res_enrich to be used for coloring the plotted gene sets. Defaults sensibly to z_score.
return_barchart	Logical, whether to return a barchart (instead of the default dot-segment plot); defaults to FALSE.

Value

A ggplot object

See Also

gs_summary_overview_pair(), gs_horizon()

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_summary_overview(res_enrich)

# if desired, it can also be shown as a barplot
gs_summary_overview(res_enrich, n_gs = 30, return_barchart = TRUE)

federicomarini/GeneTonic documentation built on Oct. 10, 2024, 8:49 p.m.