Trait rate map

Per-branch evolutionary rate map for a continuous trait

Command identity

Canonical command:

trait_rate_map

Handler:

trait_rate_map

Aliases:

branch_rates, rate_map

Standalone executables:

pk_trait_rate_map, pk_branch_rates, pk_rate_map

Categories:

Trait evolution

Runtime interface

Synopsis

phykit trait_rate_map --tree <tree> --trait_data <trait_data> --output <output> [--trait <trait>] [--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

--trait

false

str

none

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

Estimate per-branch evolutionary rates for a continuous trait and display them as a branch-colored phylogram. Ancestral states are reconstructed via Felsenstein's weighted-average method. Per-branch rate is the squared standardized contrast (proportional to local Brownian motion rate): rate = (child_val - parent_val)^2 / branch_length.

phykit trait_rate_map -t <tree> -d <trait_data> -o <output>
    [--trait <column>] [--json]
    [--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>]

Options:
-t/--tree: a tree file in Newick format
-d/--trait_data: tab-delimited trait file (two-column: taxon<tab>value with no header; or multi-column with header when --trait is used)
-o/--output: output plot file path (required)
--trait: column name to use from a multi-column trait file (if omitted, two-column format is expected)
--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