Phylogenetic heatmap

Phylogeny alongside a heatmap of numeric trait values

Command identity

Canonical command:

phylo_heatmap

Handler:

phylo_heatmap

Aliases:

ph, pheatmap

Standalone executables:

pk_phylo_heatmap, pk_ph, pk_pheatmap

Categories:

Trait evolution

Runtime interface

Synopsis

phykit phylo_heatmap --tree <tree> --data <data> --output <output> [--split <split>] [--standardize] [--cmap <cmap>] [--cluster-columns] [--fig-width <fig_width>] [--fig-height <fig_height>] [--dpi <dpi>] [--no-title] [--title <title>] [--legend-position <legend_position>] [--ylabel-fontsize <ylabel_fontsize>] [--xlabel-fontsize <xlabel_fontsize>] [--title-fontsize <title_fontsize>] [--axis-fontsize <axis_fontsize>] [--colors <colors>] [--ladderize] [--cladogram] [--circular] [--color-file <color_file>] [--json]

Arguments

This table is generated from the live command parser. It is the authoritative source for accepted spellings, required arguments, types, defaults, and choices.

Argument	Required	Type	Default	Choices
-t, --tree	true	str	required	any
-d, --data	true	str	required	any
-o, --output	true	str	required	any
--split	false	float	0.3	any
--standardize	false	boolean	false	any
--cmap	false	str	viridis	any
--cluster-columns	false	boolean	false	any
--fig-width	false	float	none	any
--fig-height	false	float	none	any
--dpi	false	int	300	any
--no-title	false	boolean	false	any
--title	false	str	none	any
--legend-position	false	str	none	any
--ylabel-fontsize	false	float	none	any
--xlabel-fontsize	false	float	none	any
--title-fontsize	false	float	none	any
--axis-fontsize	false	float	none	any
--colors	false	str	none	any
--ladderize	false	boolean	false	any
--cladogram	false	boolean	false	any
--circular	false	boolean	false	any
--color-file	false	str	none	any
--json	false	boolean	false	any

Output and errors

--json provides the command's structured JSON representation. Output-file options: --output. Invalid command syntax exits with status 2. Input validation and scientific limitations are described in the guidance below.

Guidance, interpretation, and examples

Draw a phylogenetic heatmap: a phylogeny alongside a color-coded matrix of numeric trait values, with rows aligned to tree tips. Analogous to R's phytools::phylo.heatmap().

phykit phylo_heatmap -t <tree> -d <data> -o <output>
        [--split 0.3] [--standardize] [--cmap viridis] [--cluster-columns] [--json]

Options:
-t/--tree: tree file (required)
-d/--data: numeric data matrix in TSV format with header row (required)
-o/--output: output figure path (required; supports .png, .pdf, .svg)
--split: fraction of figure width for the tree panel (default: 0.3)
--standardize: z-score each column before coloring
--cmap: matplotlib colormap name (default: viridis)
--cluster-columns: cluster trait columns by similarity and display a dendrogram at the top
--json: optional argument to output metadata as JSON