Density map

Posterior density of stochastic character maps

Command identity

Canonical command:

density_map

Handler:

density_map

Aliases:

densitymap, dmap

Standalone executables:

pk_density_map, pk_densitymap, pk_dmap

Categories:

Trait evolution

Runtime interface

Synopsis

phykit density_map --tree <tree> --trait_data <trait_data> --trait <trait> [--nsim <nsim>] [--seed <seed>] --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
-c, --trait	true	str	required	any
-n, --nsim	false	int	100	any
--seed	false	int	none	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 phylogram with branches colored by posterior probabilities of discrete character states from stochastic character mapping (analogous to R's phytools::densityMap()). Runs N simulations of stochastic character mapping internally and, for each point along each branch, computes the fraction of simulations in each state.

phykit density_map -t <tree> -d <trait_data> -c <trait_column> -o <output.png> [-n <nsim>] [--seed <seed>]
    [--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>state)
-c/--trait: column name of the trait to map
-o/--output: output plot file path (required)
-n/--nsim: number of stochastic mapping simulations (default: 100)
--seed: random seed for reproducibility
--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