# Getting Started: Scatterplot (tSNE or UMAP)

**URL:** <https://community.brain-map.org/t/getting-started-scatterplot-tsne-or-umap/664>\
**Category:** Transcriptomics Explorer\
**Created:** [August 12, 2020, 3:56pm UTC](https://community.brain-map.org/t/getting-started-scatterplot-tsne-or-umap/664 "2020-08-12T15:56:46Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![tylermo](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/tylermo/32/155_2.png) [@tylermo](https://community.brain-map.org/u/tylermo)\
**Post date:** [August 12, 2020, 3:56pm UTC](https://community.brain-map.org/t/getting-started-scatterplot-tsne-or-umap/664/1 "2020-08-12T15:56:47Z")

</div>

The _Scatterplot_ visualization shows each cell in the dataset in a 2D plot, generated from either the tSNE or UMAP algorithms. By default, the dots (cells) are colored by their cell type assignment. At a glance, most cells in a single type are visually grouped together in tSNE space, but not all. Zoom in/out and pan to examine cell types of interest.

Click on a cell to highlight all cells of the same type.

 ![image](https://canada1.discourse-cdn.com/flex027/uploads/brainobservatory/original/1X/217e56206c47e124250aac842582c25c97f68cc0.png)

**Examine Gene Expression in tSNE space**  
To color the cells by expression of a gene, click the “Color By” menu near the top left of the screen.  
 ![image](https://canada1.discourse-cdn.com/flex027/uploads/brainobservatory/original/1X/bc7e02a3cc601bfd13ba6257d92537f37fd0653f.png)

Choose a gene that you already have on the heatmap, or search for a gene using gene symbol.

 ![image](https://canada1.discourse-cdn.com/flex027/uploads/brainobservatory/original/1X/e8b42c2a3fbf8a680aa1e1f42d65aad7952c9da0.png)

Alternatively, color the tSNE by gene expression directly from the Heatmap view. Click the gene symbol in the heatmap view, and choose _Color t-SNE with expression of_ . ![image](https://canada1.discourse-cdn.com/flex027/uploads/brainobservatory/original/1X/86bb9d09af1a102e291e08723270d967a31312e2.png)

**Gene Expression Histogram**  
When the scatterplot is colored by gene expression, you can select a cell type to see a histogram of gene expression for all cells in that type.

 ![image](https://canada1.discourse-cdn.com/flex027/uploads/brainobservatory/original/1X/498f164b25c282bfe626258459baeba89fb041f9.png)

**Customize Visualization**  
Change the color map by clicking on the current selection in the bottom of the screen.

 ![image](https://canada1.discourse-cdn.com/flex027/uploads/brainobservatory/original/1X/02a4d9d0cce861b651260c24126be57fc877474b.png)