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Update 0008-04-01-DE_analysis.md
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ksinghal28 committed Apr 30, 2024
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Expand Up @@ -45,7 +45,7 @@ FeaturePlot(merged, features = 'Epcam') +
DimPlot(merged, group.by = 'immgen_singler_main', label = TRUE)
```

While the plots generated by the above commands make it pretty clear that the clusters of interest are clusters 8 and 12, sometimes it is trickier to determine which cluster we are interested in solely from the UMAP as the clusters may be overlapping. In this case, a violin plot `VlnPlot` may be more helpful. Similar to `FeaturePlot`, `VlnPlot` also takes the Seurat object and `features` as input. It also requires a `group.by` argument that determines the x-axis groupings of the cells.
While the plots generated by the above commands make it pretty clear that the clusters of interest are clusters 9 and 12, sometimes it is trickier to determine which cluster we are interested in solely from the UMAP as the clusters may be overlapping. In this case, a violin plot `VlnPlot` may be more helpful. Similar to `FeaturePlot`, `VlnPlot` also takes the Seurat object and `features` as input. It also requires a `group.by` argument that determines the x-axis groupings of the cells.
To learn more about customizing a Violin plot, please refer to the [Seurat documentation](https://satijalab.org/seurat/reference/vlnplot)

```R
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