gs_summary_overview {GeneTonic}R Documentation

Plots a summary of enrichment results

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",
  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).

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, 30, return_barchart = TRUE)

[Package GeneTonic version 1.4.1 Index]