sig_heatmap {ideal} | 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

    sig_heatmap(
      vst_data,
      my_signature,
      res_data = NULL,
      FDR = 0.05,
      de_only = FALSE,
      annovec,
      title = "",
      cluster_rows = TRUE,
      cluster_cols = FALSE,
      anno_colData = NULL,
      center_mean = TRUE,
      scale_row = FALSE
    )

### Arguments

`vst_data` | A `DESeqTransform` object - usually the variance stabilized transformed data, which will be used to extract the expression values
`my_signature` | A character vector, usually named, containing the genes which compose the gene signature
`res_data` | A `DESeqResults` object. If not provided, it can be computed during the execution of the application
`FDR` | Numeric value between 0 and 1, the False Discovery Rate
`de_only` | Logical, whether to display only DE genes belonging to the pathway - defaults to FALSE
`annovec` | A named character vector, with the corresponding annotation across IDs
`title` | Character, title for the heatmap
`cluster_rows` | Logical, whether to cluster rows - defaults to TRUE
`cluster_cols` | Logical, whether to cluster column - defaults to FALSE. Recommended to be set to TRUE if de_only is also set to TRUE
`anno_colData` | Character vector, specifying the elements of the colData information to be displayed as a decoration of the heatmap. Can be a vector of any length, as long as these names are included as colData. Defaults to NULL, which would plot no annotation on the samples.
`center_mean` | Logical, whether to perform mean centering on the expression values. Defaults to TRUE, as it improves the general readability of the heatmap
`scale_row` | Logical, whether to perform row-based standardization of the expression values

### Value

A plot based on the `pheatmap` function

### Examples

    # with the well known airway package...
    library(airway)
    data(airway)
    airway
    dds_airway <- DESeq2::DESeqDataSetFromMatrix(assay(airway),
      colData = colData(airway),
      design = ~ cell + dex
    )
    ## Not run:
    dds_airway <- DESeq2::DESeq(dds_airway)
    res_airway <- DESeq2::results(dds_airway)
    vst_airway <- DESeq2::vst(dds_airway)
    library(org.Hs.eg.db)
    annovec <- mapIds(org.Hs.eg.db, rownames(dds_airway), "ENTREZID", "ENSEMBL")
    mysignatures <- read_gmt(
      "http://data.wikipathways.org/20190210/gmt/wikipathways-20190210-gmt-Homo_sapiens.gmt"
    )
    mysignature_name <- "Lung fibrosis%WikiPathways_20190210%WP3624%Homo sapiens"
    library(pheatmap)
    sig_heatmap(vst_airway,
      mysignatures[[mysignature_name]],
      res_data = res_airway,
      de_only = TRUE,
      annovec = annovec,
      title = mysignature_name,
      cluster_cols = TRUE
    )

    ## End(Not run)

[Package ideal version 1.18.1 Index]