pheatmap

Pheatmap is an R package that provides a user-friendly interface for generating enhanced heatmaps, with built-in support for annotations, clustering, and customizable aesthetics. It was developed to offer a convenient alternative to traditional heatmap plotting functions and is widely used in fields such as genomics and transcriptomics. The package is available on CRAN and is commonly used in data exploration and visualization workflows.

Key features of pheatmap include the ability to cluster rows and columns using hierarchical clustering with configurable distance measures and linkage methods. It supports annotation tracks for rows and columns through annotation_row and annotation_col objects, allowing additional metadata to be shown alongside the heatmap. Colors and scales are highly customizable, with options to apply a row or column scale, choose color palettes, and control breaks. Other useful options include displaying row and column names, adjusting cell size, adding numbers inside cells, and controlling dendrogram display with treeheight_row and treeheight_col. The function also supports saving output directly to files via filename, width, height, and other graphical parameters.

Input to pheatmap is typically a numeric matrix or data frame, with NA values allowed. The function returns a list containing the clustering results, the heatmap object, and the data used, which can be inspected for reproducibility or further analysis. Users can also supply annotation data frames and a named color list to customize annotation colors.

Example usage: library(pheatmap); pheatmap(mat); pheatmap(mat, scale="row", clustering_distance_rows="euclidean", clustering_method="complete"); pheatmap(mat, annotation_col=annotation_col, display_numbers=TRUE).