Abundance Column Percent

Normalize a taxa-by-sample abundance matrix to percentages within each sample column.

Description

Abundance percentages compare taxa within each sample.

Abundance percentages compare taxa within each sample. A taxa-by-sample matrix requires normalization by columns rather than rows.

Normalize a taxa-by-sample abundance matrix to percentages within each sample column.

When to use Abundance Column Percent

Use this for the following task: Normalize a taxa-by-sample abundance matrix to percentages within each sample column.

Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.

How to use Abundance Column Percent and understand its results

Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
Enter taxonSampleCounts using the field table, then run the tool.
Read columnTotals, abundancePercent. Interpret flags, units, ordering and placeholder values using the rules below.
Review any reported issue or failed check, correct the supplied values when appropriate, and verify the result in its intended context.

Input field	Meaning	Value type and bounds	Requirement
taxonSampleCounts	Taxon sample counts	list of list of number; minimum entries 1; maximum entries 128; each entry: list of number; minimum entries 1; maximum entries 128; each entry: number; minimum 0	Required

Supply a rectangular nonnegative matrix with positive finite totals for every sample column. Sum columns and divide each cell by its own sample total.^[1]

percent[i,j] = 100 count[i,j]/columnTotal[j]

This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.

Output field	Meaning	Value type
columnTotals	Column totals	list of number
abundancePercent	Abundance percent	list of list of number

json

{
  "input": {
    "taxonSampleCounts": [
      [
        1,
        3
      ],
      [
        3,
        1
      ]
    ]
  },
  "output": {
    "columnTotals": [
      4,
      4
    ],
    "abundancePercent": [
      [
        25,
        75
      ],
      [
        75,
        25
      ]
    ]
  }
}

Limitations and assumptions

Rows must refer to the same taxa. Percentages do not correct detection bias or convert counts to absolute abundance.

The tool operates on supplied local data; alignment, filtering and annotation must already be appropriate for the stated calculation. Malformed requests produce input errors. A successfully evaluated request can still contain false flags, empty result lists or a result outside the supplied threshold; those outcomes have the meanings stated above.

Alternative or Complementary methods

Choose Bray Curtis Sample Matrix for this operation: Build a Bray–Curtis pairwise dissimilarity matrix for samples with aligned taxa. For a complementary task, use On Target Read Efficiency for this operation: Compute capture efficiency as the fraction of mapped reads overlapping targets.

The implementation reference documents the exact calculation, supported input shapes and returned fields.

References

Abundance Column Percent — tool.io

Similar or alternative tools

Bray Curtis Sample Matrix
Build a Bray–Curtis pairwise dissimilarity matrix for samples with aligned taxa.
On Target Read Efficiency
Compute capture efficiency as the fraction of mapped reads overlapping targets.