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Heatmap Visualization

heatmap_function.Rd

Heatmap Visualization

Usage

heatmap_function(
  initial_table,
  table_list,
  ensembl_dataset = "hsapiens_gene_ensembl",
  orgdb = org.Hs.eg.db
)

Arguments

initial_table

A DESeq2 dataset (DESeqDataSet) containing the normalized count data and sample metadata used to construct the heatmap.

table_list

A data frame or tibble containing the differential expression results generated by the differential expression analysis. The table must contain the gene identifiers required to match genes in initial_table.

ensembl_dataset

Keyword for Ensembl database. Default is "hsapiens_gene_ensembl".

orgdb

Organism database. Default is human: org.Hs.eg.db. Other organism annotation databases are available from https://bioconductor.org/packages/3.23/data/annotation/.

Value

A ComplexHeatmap::Heatmap object displaying the scaled log-normalized expression values of the selected DEGs.

Details

Visualizes scaled (z-scored) log-normalized expression counts for differentially expressed genes (DEGs) using ComplexHeatmap.

Expression counts are extracted from the supplied DESeq2 object, log-normalized, and scaled by gene prior to visualization. Genes identified in the supplied DEG table are used to construct the heatmap.

The heatmap is configured to perform hierarchical clustering of both rows and columns. Gene identifiers are not converted within this function. Gene ID conversion should be performed separately using bulkanalysis::gene_id_converter_ver2().

The expression matrix is transformed to log-normalized counts and subsequently z-scored across genes before visualization. Each row therefore represents the relative expression pattern of a gene across samples.

Rows and columns are hierarchically clustered by default. Gene identifiers are retained in their original format and are not converted to external gene names within this function.

See also

ComplexHeatmap::Heatmap, bulkanalysis::gene_id_converter_ver2

Examples

if (FALSE) { # \dontrun{
heatmap <- heatmap_visualization(
  initial_table = dds,
  DEG_table = deg_results
)
} # }