gs_summary_overview: Plots a summary of enrichment results

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

Description

Plots a summary of enrichment results for one set

Usage

gs_summary_overview(
  res_enrich,
  n_gs = 20,
  p_value_column = "gs_pvalue",
  color_by = "z_score"
)

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).
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.

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)

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