amalgkit csfilter

Overview

amalgkit csfilter performs cross-species outlier filtering using ortholog information. It writes filtered metadata, excluded-row summaries, and cross-species QC plots.

csfilter is Python-only.

Inputs

csfilter expects:

• filtered or unfiltered metadata
• abundance tables from merge or cstmm
• one ortholog source

Provide one of:

• --dir_busco
• --orthogroup_table

If --input_dir inferred is used, AMALGKIT reads:

out_dir/cstmm if it exists, otherwise out_dir/merge

Basic Use

After wsfilter:

amalgkit csfilter \
    --out_dir ./ \
    --metadata ./wsfilter/metadata.tsv \
    --dir_busco ./busco

Without wsfilter:

amalgkit csfilter \
    --out_dir ./ \
    --metadata ./metadata/metadata.tsv \
    --dir_busco ./busco

Using an orthogroup table:

amalgkit csfilter \
    --out_dir ./ \
    --metadata ./wsfilter/metadata.tsv \
    --orthogroup_table ./Orthogroups.tsv

Main Outputs

• csfilter/metadata.tsv
• csfilter/excluded.tsv
• csfilter/csfilter_exclusion.pdf
• csfilter/csfilter_overview.pdf
• csfilter/csfilter_unaveraged_pca_PC12.pdf
• csfilter/csfilter_heatmap.pdf
• csfilter/csfilter_within_group_cor.pdf
• csfilter/csfilter_outlier_scatter.pdf

Useful Options

Option	Default	Use
--missing_strategy	em_pca	missing-value handling before dimensionality reduction
--norm	log2p1-fpkm	expression transformation used for temporary tables
--margin_threshold	0.0	robust-margin threshold
--robust_z_threshold	-2.5	robust z-score threshold
--sample_group	all groups	comma-separated sample groups to include
--sample_group_color	automatic	colors for selected sample groups

Chaining

amalgkit wsfilter --out_dir ./
amalgkit csfilter \
    --out_dir ./ \
    --metadata ./wsfilter/metadata.tsv \
    --dir_busco ./busco
amalgkit finalize \
    --out_dir ./ \
    --metadata ./csfilter/metadata.tsv \
    --batch_effect_alg sva