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Don't use default assay name for Seurat objects #507

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Merged
aaronwolen merged 2 commits into from
Nov 7, 2022
Merged

Don't use default assay name for Seurat objects #507

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3dc5006
Explicitly pass assay name when recreating Seurat object
aaronwolen Nov 4, 2022
393026b
Update news and bump version
aaronwolen Nov 4, 2022
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2 changes: 1 addition & 1 deletion apis/r/DESCRIPTION
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Expand Up @@ -7,7 +7,7 @@ Description: Interface for working with 'TileDB'-based Stack of Matrices,
from and export to in-memory formats used by popular toolchains like
'Seurat', 'Bioconductor', and even 'AnnData' using the companion Python
package.
Version: 0.1.12
Version: 0.1.12.9000
Authors@R: c(
person(given = "Aaron",
family = "Wolen",
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5 changes: 5 additions & 0 deletions apis/r/NEWS.md
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@@ -1,3 +1,8 @@
# tiledbsoma (development version)

## Fixes
* Don't use default assay name when recreating a `Seurat` object (thanks @dan11mcguire)

# tiledbsoma 0.1.12

## Package name
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7 changes: 4 additions & 3 deletions apis/r/R/SOMACollection.R
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Expand Up @@ -215,16 +215,17 @@ SOMACollection <- R6::R6Class(
obs_df <- self$somas[[1]]$obs$to_dataframe()

# retain cell identities before restoring cell-level metadata
idents <- obs_df$active_ident
idents <- obs_df$active_ident
if (!is.null(idents)) {
idents <- setNames(idents, rownames(obs_df))
idents <- stats::setNames(idents, rownames(obs_df))
obs_df$active_ident <- NULL
}

object <- SeuratObject::CreateSeuratObject(
counts = assays[[1]],
project = project,
meta.data = obs_df
meta.data = obs_df,
assay = names(assays)[1]
)

if (!is.null(idents)) {
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