enhance_table {GeneTonic} | R Documentation

## 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_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_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
    )

[Package GeneTonic version 1.4.1 Index]