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Skip Batch UMAP if Theres No Batch Column in Metadata #2

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Skip Batch UMAP if Theres No Batch Column in Metadata #2

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23 changes: 14 additions & 9 deletions modules/local/seurat/cluster/notebook_seurat_clustering.qmd
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Original file line number Diff line number Diff line change
Expand Up @@ -400,15 +400,20 @@ The @fig-umap-sample sample-based UMAP can be used to evaluate cluster compositi
#| fig-height: 10
#| fig-align: center

SCP::CellDimPlot(
srt = seurat_object,
group.by = "batch",
reduction = "umap",
label = TRUE,
label_repel = TRUE,
show_stat = TRUE,
theme_use = "theme_blank"
)
# Skip step if batch column does not exists in metadata
if("batch" %in% metadata_columns) {
SCP::CellDimPlot(
srt = seurat_object,
group.by = "batch",
reduction = "umap",
label = TRUE,
label_repel = TRUE,
show_stat = TRUE,
theme_use = "theme_blank"
)
} else {
print("Batch column not found in metadata")
}

```

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