signature_volcano: Plot a volcano plot of a geneset

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

Plot a volcano plot of a geneset

Description

Plot a volcano plot for the geneset of the provided data, with the remaining genes as shaded dots in the background of the plot.

Usage

signature_volcano(
  res_de,
  res_enrich,
  annotation_obj = NULL,
  gtl = NULL,
  geneset_id = NULL,
  genelist = NULL,
  FDR = 0.05,
  color = "#1a81c2",
  volcano_labels = 25,
  plot_title = NULL
)

Arguments

res_de	A DESeqResults object.
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).
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.
geneset_id	Character specifying the gene set identifier to be plotted.
genelist	A vector of character strings, specifying the identifiers contained in the rownames of the res_de input object.
FDR	Numeric value, specifying the significance level for thresholding adjusted p-values. Defaults to 0.05.
color	Character string to specify color of filtered points in the plot. Defaults to #1a81c2 (shade of blue).
volcano_labels	Integer, maximum number of labels for the gene sets to be plotted as labels on the volcano scatter plot. Defaults to 25.
plot_title	Character string, to specify the title of the plot, displayed over the volcano plot. If left to NULL as by default, it tries to use the information on the geneset identifier provided.

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)

signature_volcano(res_de,
  res_enrich,
  anno_df,
  geneset_id = res_enrich$gs_id[1]
)

# alternatively

chemokine_list <- c(
  "ENSG00000108702",
  "ENSG00000172156",
  "ENSG00000181374",
  "ENSG00000276409"
)

signature_volcano(res_de,
  res_enrich,
  anno_df,
  genelist = chemokine_list
)

federicomarini/GeneTonic documentation built on Dec. 21, 2024, 10:05 p.m.