[YoukaiFromAccounting]

Fixes #9142

This PR fixes LoadXenium() for standalone gene panels containing only Gene Expression features.

Read10X_h5() normally returns a named list when multiple feature types are present (ie: gene expression, negative control probes, negative control codewords), but returns a bare dgCMatrix when only one feature type is present. LoadXenium() had previously assumed data$matrix was always a list and attempted to access data$matrix[["Gene Expression"]], which would result in the following error when using LoadXenium to load in standalone gene panels:

Error in `CreateAssayObject()`:
! No cell names (colnames) names present in the input matrix

This PR makes a small change in LoadXenium() to use the matrix directly when data$matrix is not a list, while defaulting to the existing behaviour for datasets with multiple feature types.

Reproducible example

library(Seurat)
library(Matrix)

counts <- sparseMatrix(
  i = c(1, 2),
  j = c(1, 2),
  x = c(1, 1),
  dimnames = list(
    c("Gene1", "Gene2"),
    c("Cell1", "Cell2")
  )
)

data <- list(matrix = counts)

class(data$matrix)
is.list(data$matrix)

# Previous behavior of counts = data$matrix[["Gene Expression"]] (used in LoadXenium) will error
data$matrix[["Gene Expression"]]

This fix was adapted from prior changes suggested by @BenjaminDEMAILLE in #10489.

[Copilot]

🟡 Changes recommended

A regression test for standalone single-feature Xenium panels is missing.

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Pull request overview

Fixes LoadXenium() for standalone Xenium gene panels by supporting bare sparse matrices returned when only one feature type is present.

Changes:

• Uses the matrix directly for non-list inputs.
• Preserves existing extraction for multi-feature lists.

File summaries

File	Description
R/convenience.R	Updates Xenium count-matrix selection.

Review details

• Files reviewed: 1/1 changed files
• Comments generated: 1
• Review effort level: Lite

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