enhance_table: Visually enhances a functional enrichment result table

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

Visually enhances a functional enrichment result table

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,
  gtl = NULL,
  n_gs = 50,
  gs_ids = NULL,
  chars_limit = 70,
  plot_style = c("point", "ridgeline"),
  ridge_color = c("gs_id", "gs_score"),
  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.
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.
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_style	Character value, one of "point" or "ridgeline". Defines the style of the plot to summarize visually the table.
ridge_color	Character value, one of "gs_id" or "gs_score", controls the fill color of the ridge lines. If selecting "gs_score", the z_score column must be present in the enrichment results table - see get_aggrscores() to do that.
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
)

# using the ridge line as a style, also coloring by the Z score
res_enrich_withscores <- get_aggrscores(
  res_enrich,
  res_de,
  anno_df
)
enhance_table(res_enrich_withscores,
  res_de,
  anno_df,
  n_gs = 10, 
  plot_style = "ridgeline",
  ridge_color = "gs_score"
)

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