gs_alluvial {GeneTonic} | R Documentation

## Alluvial (sankey) plot for a set of genesets and the associated genes

### Description

Generate an interactive alluvial plot linking genesets to their associated genes

### Usage

    gs_alluvial(res_enrich, res_de, annotation_obj, n_gs = 5, gs_ids = NULL)

    gs_sankey(res_enrich, res_de, annotation_obj, n_gs = 5, gs_ids = 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`.
`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.

### Value

A `plotly` 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)

    gs_alluvial(res_enrich = res_enrich,
                res_de = res_de,
                annotation_obj = anno_df,
                n_gs = 4)
    # or using the alias...
    gs_sankey(res_enrich = res_enrich,
              res_de = res_de,
              annotation_obj = anno_df,
              n_gs = 4)

[Package GeneTonic version 1.2.0 Index]