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Sample metadata#

Sample metadata (demographics, clinical data, lab values, …) to the NPX data, and see exactly which IDs have no match.

add_sample_info#

Add the columns of your sample metadata to the NPX data, and report every ID without a match.

add_sample_info(npx, samples, *, on, npx_on="SampleID",
                verbose=True) -> pandas.DataFrame

Inputs

Argument Type Default Meaning
npx DataFrame — table from read_npx
samples DataFrame, or path to a .csv / .xlsx file — your sample metadata, one row per sample
on str — the column in your sample metadata holding the same IDs as the NPX data (e.g. "FIF ID")
npx_on str "SampleID" the ID column in the protein data
verbose bool True print the matching report

Output. The protein table with:

  • every column of your sample metadata added. NPX rows without a match are kept, with empty sample metadata;
  • a column sample with the tidy ID used for matching: spaces at the ends removed, capitals, and spaces, underscores and hyphens treated the same, so "308 BIS", "308_bis" and "308-BIS" all become "308_BIS". Leading zeros are kept ("058" stays "058"). apply_qc and the bridging functions match IDs the same way;
  • the ending _samplelist on sample-list columns whose name already exists in the protein data (e.g. PlateID_samplelist).

The matching report is stored in df.attrs["sample_report"]. It lists:

  • how many samples matched, and how many only after tidying the IDs;
  • which IDs are only in the protein data (marked WARNING);
  • which IDs are only in your sample metadata.

Errors

  • KeyError: on is missing from your sample metadata, or npx_on from the NPX data.
  • ValueError: your sample metadata have the same ID twice (after tidying). Each sample may appear once.

Example

data = so.add_sample_info(plates, "2025.05.08_sample_manifest.xlsx", on="FIF ID")

Matching report
  matched on: SampleID (NPX data) = FIF ID (your sample metadata)
  matched: 142 of 143 sample IDs in the NPX data
  WARNING missing from your sample metadata (kept, without sample metadata): 249
  columns in both tables (yours renamed with the ending _samplelist): PlateID