signature_volcano {GeneTonic} | R Documentation

## 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 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)
    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
    )

[Package GeneTonic version 1.4.1 Index]