Add sampleData argument to store multi sample's metadata information (bulk, single-cell, spatial) in se object

[lingminhao]

This PR allows the user to provide sample-specific metadata using the sampleData argument.

Format Supported:

• Bulk Data: one single .csv metadata file with a mandatory sampleName column is sufficient. Every row then contains metadata information for a sample. Multiple .csv file for each sample is possible, but not necessary.
• Single-Cell / Spatial Data: one .csv metadata file per single-cell/spatial sample, each containing a mandatory barcode column.

If a specific sample lacks metadata, users can simply pass a NA value at the corresponding index in the input vector (e.g., c("metadata_sample1.csv", NA, "metadata_sample3.csv")).

Users can then define any additional metadata columns as needed in the metadata .csv file. The metadata will be stored in the colData of the se SummarizedExperiment object

[Copilot]

Pull request overview

Adds a sampleData argument to bambu() to allow users to attach per-sample (bulk) or per-sample/per-barcode (single-cell/spatial) metadata from CSV files into the output SummarizedExperiment’s colData.

Changes:

• Adds sampleData to bambu() and threads it into assignReadClasstoTranscripts().
• Reworks generateColData() to left-join user-provided CSV metadata by sampleName (bulk) or barcode (demultiplexed).
• Changes multi-sample SE assembly to carry forward per-sample colData into the combined SE.

Reviewed changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated 9 comments.

Show a summary per file

File	Description
R/bambu.R	Adds sampleData param and passes it through quantification path; changes how combined colData is built.
R/bambu-assignDist.R	Extends assignReadClasstoTranscripts() signature to accept sampleData and uses new generateColData().
R/bambu_utilityFunctions.R	Updates combineCountSes() to accept external colData list and rewrites generateColData() to join CSV metadata.
R/bambu-processReads_utilityConstructReadClasses.R	Formatting/brace cleanup in read-class construction.
R/bambu-processReads.R	Removes an unused warnings placeholder variable.

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[ch99l]

After the requested code changes, code runs as expected.

[jonathangoeke]

can you add a comment on the expected pattern? that will help to understand this line/change if needed

[jonathangoeke]

ColNames should be identical to the names of the colData? otherwise there is a mismatch between sample names in colData and in assays?

[ch99l]

Code works incorrectly for visium HD samples due to regex as the barcodes have this format: s_002um_xpos_ypos

Instead of regex, use information extracted in the CB column previously (refer to prepareDataFromBam.R)