Document blobplot taxonomic rank parameters

[Mirochill]

Summary

• document how to use --param catField=<taxrule>_<rank> when exporting blob plots from the command line
• add examples for family/genus-level blob plot exports in the commands reference and tutorial
• clarify that default taxonomic fields from the default taxrule are named like bestsumorder_phylum, bestsumorder_family, and bestsumorder_genus

Fixes #277

Validation

• Not run locally
• Static validation only: git diff --check

Summary by Sourcery

Document how to select taxonomic rank-specific category fields when exporting blob plots from the command line.

Documentation:

• Explain default taxrule-derived category field names used for blob plots (e.g. bestsumorder_phylum, bestsumorder_family, bestsumorder_genus).
• Add command reference examples showing use of the catField parameter to render blob plots at different taxonomic ranks from the CLI.
• Extend the tutorial with a step demonstrating blob plot export at alternate taxonomic ranks using catField.

[sourcery-ai]

Reviewer's Guide

Documents how to use the catField parameter to control taxonomic rank for blob plot exports and adds concrete family/genus examples to both the command reference and tutorial.

Flow diagram for blobtools view export with catField taxonomic rank override

flowchart LR
    A[User runs blobtools view] --> B{catField parameter provided?}
    B -- No --> C[Use default BlobDir plot metadata catField]
    C --> D[Colour blobs by default taxrule rank
bestsumorder_phylum or existing setting]
    B -- Yes --> E[Read catField value
bestsumorder_family or bestsumorder_genus]
    E --> F[Override default category field]
    F --> G[Render/export blob plot at requested taxonomic rank]

Loading

File-Level Changes

Change	Details	Files
Clarify blobtools view export behavior and document catField usage for taxonomic ranks.	Update description of blobtools view to mention exporting BlobDir plots, not just data. Explain that default taxrule-derived taxonomic category fields follow the bestsumorder_ naming convention, with examples for phylum, family, and genus. Add a CLI example showing blob plot export using --param catField=bestsumorder_family via the --plot path. Add a CLI example showing blob plot export using --param catField=bestsumorder_genus via the viewer-backed export path (without --plot).	docs/command-line/commands.md
Extend the command-line tutorial with a step showing blob plot export at alternate taxonomic ranks using catField.	Introduce a new tutorial step explaining that blob plots use the BlobDir plot metadata category field by default. Document the bestsumorder_ naming pattern for default taxrule taxonomic fields in the tutorial, mirroring the command reference. Add a worked example of blobtools view --plot export specifying --param catField=bestsumorder_family. Describe how to switch to other ranks (e.g., bestsumorder_genus) to recolor blob plots by different taxonomic levels.	docs/command-line/tutorials.md

Assessment against linked issues

Issue	Objective	Addressed	Explanation
#277	Document how to generate blobplots at different taxonomic ranks (e.g., family, genus) from the command line, including which parameter to use and how taxonomic fields are named.	✅
#277	Add clear tutorial-style documentation showing example commands for exporting blobplots at different taxonomic ranks from the command line.	✅

Possibly linked issues

• Clarify how to generate blobplots with different taxonomic levels (genus, family etc) on command line #277: The PR updates docs to explain catField usage for genus/family blobplots, directly resolving the issue’s request.

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