Quartet pie chart

Phylogram with quartet concordance pie charts at internal nodes

Command identity

Canonical command:

quartet_pie

Handler:

quartet_pie

Aliases:

qpie, quartet_pie_chart

Standalone executables:

pk_quartet_pie, pk_qpie, pk_quartet_pie_chart

Categories:

Tree comparison & consensus

Runtime interface

Synopsis

phykit quartet_pie --tree <tree> [--gene-trees <gene_trees>] --output <output> [--annotate] [--branch-labels] [--csv <csv>] [--pie-size <pie_size>] [--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
-g, --gene-trees	false	str	none	any
-o, --output	true	str	required	any
--annotate	false	boolean	false	any
--branch-labels	false	boolean	false	any
--csv	false	str	none	any
--pie-size	false	float	1.0	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 phylogram with pie charts at internal nodes showing quartet concordance proportions. In native mode (-g provided), computes gene concordance factors (gCF, gDF1, gDF2) from a species tree and gene trees via bipartition matching. In ASTRAL mode (no -g), parses q1/q2/q3 annotations from ASTRAL -t 2 or wASTRAL --support 3 output.

Pie slices show concordant (blue), discordant alt 1 (red), and discordant alt 2 (gray) proportions. Use --annotate to add numeric values near each pie.

phykit quartet_pie -t <species_tree> [-g <gene_trees>] -o <output>
        [--annotate] [--branch-labels] [--csv <file>] [--ladderize] [--cladogram] [--circular] [--color-file <file>] [--json]

Options:
-t/--tree: species tree file (required)
-g/--gene-trees: gene trees file, one Newick tree per line (optional; if omitted, ASTRAL -t 2 or wASTRAL --support 3 annotations are parsed)
-o/--output: output figure path (required; supports .png, .pdf, .svg)
--annotate: show gCF/gDF values as text near each pie chart
--branch-labels: show the number of concordant gene trees (blue, above branch) and LPP support (red, below branch) on each internal branch. In ASTRAL mode, values come from f1 and pp1 annotations; in native mode, the concordant count is computed from gene trees
--csv: output per-branch concordance values (gCF, gDF1, gDF2, counts) as a CSV file
--pie-size: scale factor for pie chart size (default: 1.0; use 2.0 for double, 0.5 for half)
--colors: comma-separated colors for concordant, disc1, disc2 (default: blue, red, gray)
--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 output per-node concordance values as JSON