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small fix for ReadXenium #8298

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small fix for ReadXenium #8298

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22caa14
add `simplify = FALSE` to return df
alikhuseynov Jan 10, 2024
041cd75
quick fix
jsicherman Jan 10, 2024
85fc07f
Merge pull request #1 from jsich/js/unassigned_cw
alikhuseynov Jan 10, 2024
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5 changes: 3 additions & 2 deletions R/convenience.R
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Expand Up @@ -201,10 +201,11 @@ LoadXenium <- function(data.dir, fov = 'fov', assay = 'Xenium') {
)

xenium.obj <- CreateSeuratObject(counts = data$matrix[["Gene Expression"]], assay = assay)
if("Blank Codeword" %in% names(data$matrix))
if("Blank Codeword" %in% names(data$matrix)) {
xenium.obj[["BlankCodeword"]] <- CreateAssayObject(counts = data$matrix[["Blank Codeword"]])
else
} else if("Unassigned Codeword" %in% names(data$matrix)) {
xenium.obj[["BlankCodeword"]] <- CreateAssayObject(counts = data$matrix[["Unassigned Codeword"]])
}
xenium.obj[["ControlCodeword"]] <- CreateAssayObject(counts = data$matrix[["Negative Control Codeword"]])
xenium.obj[["ControlProbe"]] <- CreateAssayObject(counts = data$matrix[["Negative Control Probe"]])

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2 changes: 1 addition & 1 deletion R/preprocessing.R
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Expand Up @@ -2230,7 +2230,7 @@ ReadXenium <- function(
},
stop("Unknown Xenium input type: ", otype)
)
}, USE.NAMES = TRUE)
}, simplify = FALSE, USE.NAMES = TRUE)
return(data)
}

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