gs_upset: Upset plot for genesets

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

Upset plot for genesets

Description

Create an upset plot for genesets

Usage

gs_upset(
  res_enrich,
  res_de = NULL,
  annotation_obj = NULL,
  n_gs = 10,
  gtl = NULL,
  gs_ids = NULL,
  add_de_direction = FALSE,
  add_de_gsgenes = FALSE,
  col_upDE = "#E41A1C",
  col_downDE = "#377EB8",
  upset_geom = geom_point(size = 2),
  return_upsetgsg = 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).
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 included
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
gs_ids	Character vector, containing a subset of gs_id as they are available in res_enrich. Lists the gene sets to be included in addition to the top ones (via n_gs)
add_de_direction	Logical, whether to add an annotation with info on the DE direction of single genes
add_de_gsgenes	Logical, if set to TRUE adds an annotation with detail on the single components of each defined subset
col_upDE	Character, specifying the color value to be used to mark upregulated genes
col_downDE	Character, specifying the color value to be used to mark downregulated genes
upset_geom	A geom specification to be used in the upset chart. Defaults sensibly to geom_point(size = 2)
return_upsetgsg	Logical, controlling the returned value. If set to TRUE, this function will not generate the plot but only create the corresponding data.frame, in case the user wants to proceed with a custom call to create an upset plot.

Value

A ggplot object (if plotting), or alternatively a data.frame

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_upset(res_enrich,
  n_gs = 10
)

gs_upset(res_enrich,
  res_de = res_de, annotation_obj = anno_df,
  n_gs = 8,
  add_de_direction = TRUE, add_de_gsgenes = TRUE
)

# or using the practical gtl (GeneTonicList)
gtl_macrophage <- GeneTonic_list(
  dds = dds_macrophage,
  res_de = res_de,
  res_enrich = res_enrich,
  annotation_obj = anno_df
)

gs_upset(
  gtl = gtl_macrophage,
  n_gs = 15,
  add_de_direction = TRUE, add_de_gsgenes = TRUE
)

federicomarini/GeneTonic documentation built on March 27, 2024, 4:19 p.m.