> For the complete documentation index, see [llms.txt](https://documentation.panomics.bio/documentation/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://documentation.panomics.bio/documentation/analyses/analysis-workbench/sample-cell-explorer/umap.md).

# UMAP

The UMAP command in Panomics performs multiple processing steps. A [`Standard Compute`](/documentation/compute-runtimes/codeless-compute.md) runtime is required.

{% stepper %}
{% step %}

### Runs batch effect correction algorithm (optional)

| Algorithm     | Microarray           | Bulk RNA-seq w/ normalized counts | Bulk RNA-seq w/ raw counts | Single Cell RNA-seq  |
| ------------- | -------------------- | --------------------------------- | -------------------------- | -------------------- |
| Limma         | :white\_check\_mark: | :white\_check\_mark:              | :x:                        | :x:                  |
| Combat        | :white\_check\_mark: | :white\_check\_mark:              | :x:                        | :x:                  |
| CombatSeq     | :x:                  | :x:                               | :white\_check\_mark:       |                      |
| Harmony \*    | :x:                  | :x:                               | :x:                        | :white\_check\_mark: |
| scVI          | :x:                  | :x:                               | :x:                        | :white\_check\_mark: |
| {% endstep %} |                      |                                   |                            |                      |

{% step %}

### Runs PCA

{% endstep %}

{% step %}

### Computes neighborhood graph

Uses 15 neighbors and the PCA representation based on batch effect correction algorithm choice.
{% endstep %}

{% step %}

### Computes UMAP

{% endstep %}
{% endstepper %}

{% hint style="info" %}
\* The Harmony batch effect correction algorithm operates on the PCA space, so PCA is computed first and then replaced by the harmonized PCA.
{% endhint %}

In the following example, we perform normalization, then UMAP with no batch correction. Coloring the embedding by the diagnosis and sample name observations reveals strong batch effects. We then run UMAP again with Harmony batch effect correction. 

{% embed url="<https://www.loom.com/share/2d46b541ec444b708abdb40e5db65d0b?sid=032ee2b6-2775-4dba-bc67-cd0073d3d6e3>" %}
Normalize & UMAP
{% endembed %}


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