Plot a volcano plot of a geneset

Source: R/signature_volcano.R

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

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 plot returned by the ggplot() function

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)
#> using counts and average transcript lengths from tximeta
rownames(dds_macrophage) <- substr(rownames(dds_macrophage), 1, 15)
dds_macrophage <- estimateSizeFactors(dds_macrophage)
#> using 'avgTxLength' from assays(dds), correcting for library size


# 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)
)
#> 'select()' returned 1:many mapping between keys and columns

# 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)
#> Found 500 gene sets in `topGOtableResult` object.
#> Converting for usage in GeneTonic...
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]
)
#> Warning: ggrepel: 39 unlabeled data points (too many overlaps). Consider increasing max.overlaps


# alternatively

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

signature_volcano(res_de,
  res_enrich,
  anno_df,
  genelist = chemokine_list
)
#> Warning: Some of the provided gene ids were not found in the SummarizedExperiment
#> Not found: ENSG00000172156