[MMatinGerami]

Summary

Read10X_Coordinates() decided whether a tissue positions CSV has a header from the file name alone (header = basename(filename) == "tissue_positions.csv"). Files are often renamed, for example on GEO, so:

• a headed file named like the older tissue_positions_list.csv is read with its header as a data row, every column becomes character, and Read10X_Image() fails with cannot derive coordinates from non-numeric matrix (the case in Error in .local(obj, ...) : cannot derive coordinates from non-numeric matrix #9240);
• a headerless file named tissue_positions.csv silently loses its first spot.

This PR detects the header from the first line instead: in a data row the second field (in_tissue) is always 0 or 1, so the line is treated as a header otherwise (quotes are stripped first).

Type of change

• Bug fix (non-breaking change fixing an issue)
• New feature (non-breaking change adding functionality)
• Breaking change (existing functionality changed or removed)
• Documentation update
• Other (please explain below)

Motivation

Users loading Visium data downloaded from GEO keep hitting #9240 (reports up to Dec 2025), and the header assumption was identified in the issue thread.

Tests & examples

A new test in tests/testthat/test_load_10X.R writes the bundled tissue_positions_list.csv with a header under a GEO-style _list name, and without a header under the tissue_positions.csv name, and checks that both read as numeric coordinates with the right number of spots and give the same result as the original file. Before the fix 7 expectations fail (character columns; 4993 and 4991 rows instead of 4992); with the fix test_load_10X.R passes (10 tests, 66 expectations), as does test_spatial.R.

# run from tests/testthat; same test data as test_load_10X.R
src <- file.path("../testdata/visium", "spatial", "tissue_positions_list.csv")
f <- file.path(tempdir(), "GSM1_tissue_positions_list.csv")
writeLines(c("barcode,in_tissue,array_row,array_col,pxl_row_in_fullres,pxl_col_in_fullres", readLines(src)), f)
str(Read10X_Coordinates(f, filter.matrix = TRUE))
# before: imagerow chr ...; Read10X_Image() then errors
# after:  imagerow int ...

Related issues

Closes #9240

Checklist

• Branch is named appropriately (feat/*, fix/*, docs/*)
• Code follows Seurat style guidelines
• Documentation and comments have been updated (NEWS.md entry under Unreleased / Fixes)
• devtools::document() has been run (not needed: no roxygen or exported signature changed)
• devtools::check() passes with no errors or warnings (not run locally; I ran the affected test files)
• Test case demonstrating new functionality is included
• Maintainers are allowed to edit this PR