Phenogram (traitgram)

Phenogram visualizing trait evolution

Command identity

Canonical command:: phenogram
Handler:: phenogram
Aliases:: tg, traitgram
Standalone executables:: pk_phenogram, pk_tg, pk_traitgram
Categories:: Trait evolution

Runtime interface

Synopsis

phykit phenogram --tree <tree> --trait_data <trait_data> --output <output> [--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, --trait_data`	true	str	required	any
`-o, --output`	true	str	required	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

Plot a phenogram (traitgram) showing trait evolution along a phylogeny (analogous to R's phytools::phenogram()). The X-axis represents distance from the root and the Y-axis represents trait values. Ancestral states are reconstructed via maximum-likelihood.

phykit phenogram -t <tree> -d <trait_data> -o <output.png>
    [--fig-width <float>] [--fig-height <float>] [--dpi <int>] [--no-title] [--title <str>]
    [--legend-position <str>] [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
    [--title-fontsize <float>] [--axis-fontsize <float>] [--colors <str>] [--ladderize] [--cladogram] [--circular] [--color-file <file>] [--json]

Options:
-t/--tree: a tree file in Newick format
-d/--trait_data: tab-delimited trait file (taxon<tab>value)
-o/--output: output plot file path (required)
--fig-width: figure width in inches (auto-scaled if omitted)
--fig-height: figure height in inches (auto-scaled if omitted)
--dpi: resolution in DPI (default: 300)
--no-title: hide the plot title
--title: custom title text
--legend-position: legend location (e.g., "upper right", "none" to hide)
--ylabel-fontsize: font size for y-axis labels; 0 to hide
--xlabel-fontsize: font size for x-axis labels; 0 to hide
--title-fontsize: font size for the title
--axis-fontsize: font size for axis labels
--colors: comma-separated colors (hex or named)
--ladderize: ladderize (sort) the tree before plotting
--cladogram: draw cladogram (equal branch lengths, tips aligned) instead of phylogram
--circular: draw circular (radial/fan) phylogram instead of rectangular
--color-file: color annotation file for tip labels, clade ranges, and branch colors (iTOL-inspired TSV format)
--json: optional argument to print results as JSON