R: Plot a heatmap of the gene signature on the data

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,
  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
`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 1.11.2 Index]