Plot alignment QC

Visual quality control plots for alignments

Command identity

Canonical command:

plot_alignment_qc

Handler:

plot_alignment_qc

Aliases:

paqc, plot_qc

Standalone executables:

pk_plot_alignment_qc, pk_paqc, pk_plot_qc

Categories:

Alignment quality & statistics

Runtime interface

Synopsis

phykit plot_alignment_qc <alignment> [--output <output>] [--width <width>] [--height <height>] [--dpi <dpi>] [--gap-z <gap_z>] [--composition-z <composition_z>] [--distance-z <distance_z>] [--rcvt-z <rcvt_z>] [--occupancy-z <occupancy_z>] [--entropy-z <entropy_z>] [--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

alignment

true

str

required

any

-o, --output

false

str

alignment_qc.png

any

--width

false

float

14.0

any

--height

false

float

10.0

any

--dpi

false

int

300

any

--gap-z

false

float

3.0

any

--composition-z

false

float

3.0

any

--distance-z

false

float

3.0

any

--rcvt-z

false

float

3.0

any

--occupancy-z

false

float

3.0

any

--entropy-z

false

float

3.0

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

Generate a multi-panel alignment quality-control plot.

The figure includes: 1) occupancy per taxon
2) gap rate per taxon
3) composition distance vs long-branch proxy scatter
4) count of flagged outliers by feature

Outlier evaluation uses the same features as alignment_outlier_taxa: gap_rate, occupancy, composition_distance, long_branch_proxy, rcvt, and entropy_burden.

phykit plot_alignment_qc <alignment> [-o/--output <path>] [--width <float>] [--height <float>] [--dpi <int>] [--gap-z <float>] [--composition-z <float>] [--distance-z <float>] [--rcvt-z <float>] [--occupancy-z <float>] [--entropy-z <float>] [--json]

Options:
<alignment>: first argument after function name should be an alignment file
-o/--output: output image path (default: alignment_qc.png)
--width: figure width in inches (default: 14.0)
--height: figure height in inches (default: 10.0)
--dpi: output image DPI (default: 300)
--gap-z: z-threshold for gap-rate outliers (default: 3.0)
--composition-z: z-threshold for composition-distance outliers (default: 3.0)
--distance-z: z-threshold for long-branch-proxy outliers (default: 3.0)
--rcvt-z: z-threshold for RCVT outliers (default: 3.0)
--occupancy-z: z-threshold for low-occupancy outliers (default: 3.0)
--entropy-z: z-threshold for entropy-burden outliers (default: 3.0)
--json: optional argument to print plot metadata and outlier summary as JSON