gs_heatmap {GeneTonic} | R Documentation

## Plot a heatmap of the gene signature on the data

### Description

Plot a heatmap for the selected gene signature on the provided data, with the possibility to compactly display also DE only genes

### Usage

    gs_heatmap(
      se,
      res_de,
      res_enrich,
      annotation_obj = NULL,
      gtl = NULL,
      geneset_id = NULL,
      genelist = NULL,
      FDR = 0.05,
      de_only = FALSE,
      cluster_rows = TRUE,
      cluster_columns = FALSE,
      center_mean = TRUE,
      scale_row = FALSE,
      anno_col_info = NULL,
      plot_title = NULL,
      ...
    )

### Arguments

`se` | A `SummarizedExperiment` object, or an object derived from this class, such as a `DESeqTransform` object (variance stabilized transformed data, or regularized logarithm transformed), in where the transformation has been applied to make the data more homoscedastic and thus a better fit for visualization.
`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 row names of the `se` input object.
`FDR` | Numeric value, specifying the significance level for thresholding adjusted p-values. Defaults to 0.05.
`de_only` | Logical, whether to include only differentially expressed genes in the plot
`cluster_rows` | Logical, determining if rows should be clustered, as specified by `ComplexHeatmap::Heatmap()`
`cluster_columns` | Logical, determining if columns should be clustered, as specified by `ComplexHeatmap::Heatmap()`
`center_mean` | Logical, whether to perform mean centering on the row-wise
`scale_row` | Logical, whether to standardize by row the expression values
`anno_col_info` | A character vector of names in `colData(dds)` to use for decorating the heatmap as annotation.
`plot_title` | Character string, to specify the title of the plot, displayed over the heatmap. If left to `NULL` as by default, it tries to use the information on the geneset identifier provided
`...` | Additional arguments passed to other methods, e.g. in the call to `ComplexHeatmap::Heatmap()`

### Value

A plot returned by the `ComplexHeatmap::Heatmap()` 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)

    vst_macrophage <- vst(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_heatmap(vst_macrophage,
      res_de,
      res_enrich,
      anno_df,
      geneset_id = res_enrich$gs_id[1],
      cluster_columns = TRUE,
      anno_col_info = "condition"
    )

[Package GeneTonic version 1.4.1 Index]