Load a table of embedding coordinates (one row per cell).
Columns like UMAP_1 / UMAP_2 or tSNE_1 / tSNE_2 are auto-detected,
plus a cluster / cell-type column to color by.
Use Browse file, drop a CSV / TSV, or click Demo Data.
What this tool does
This is a viewer for precomputed 2D embeddings. It plots coordinates you already generated (UMAP, t-SNE, PHATE, or any two numeric columns) — it does not run the embedding itself. Compute the embedding in Scanpy, Seurat, or scikit-learn, then plot and style it here.
Input format
CSV or TSV with one row per cell/point. Include two coordinate columns (e.g. UMAP_1, UMAP_2) and any metadata columns. An optional first text column is used as the point ID in tooltips.
Coordinates
The X and Y columns are auto-detected from common names (UMAP, tSNE, PHATE, dim1/dim2, x/y). Override them with the Coordinates selectors.
Color
Color by a categorical column (cluster, cell type) for a discrete legend, or by a numeric column (gene expression, QC metric) for a continuous colormap with a colorbar. For numeric columns you can switch between categorical and continuous, and clip the color range to percentiles to tame outliers.
Cluster labels
With categorical coloring, group names are drawn at each group's median position. Toggle with "Show cluster labels".
Zoom, pan, and select
Scroll to zoom, drag to pan, and use ⟳ to reset the view. Hover a point to inspect it; click to select. Click a group's dot in the Groups panel to hide or show that cluster.
Large datasets
Up to 500,000 points are held in the browser. For responsiveness the plot draws a density-preserving random subsample (about 150,000 points); tick "Draw all points" to render every stored point. Files larger than 500,000 rows are randomly subsampled on load.
Equal aspect ratio
Embedding axes share one scale, so the plot keeps a 1:1 aspect ratio by default — turn it off to stretch the plot to fill the canvas.
Export
PNG honors the DPI selector (300 is publication standard). SVG is vector; dense scatters embed the points as a high-resolution raster layer while axes, labels, legend, and colorbar stay editable vector. Copy puts a PNG on the clipboard. Exports capture the current zoom/pan view.
If this tool was useful in your work, please cite it as:
EuropaDX, Inc. (2026). UMAP / t-SNE Plotter — EuropaXp OmicsCloud Bioinformatics Toolkit. Available at https://europadx.com/tools/umap/The plotter runs entirely client-side and holds up to ~500,000 points in the browser. Larger datasets are randomly subsampled on load, which may hide rare populations.
EuropaXp OmicsCloud handles datasets of any size with full single-cell pipelines, persistent workspaces, and reproducible reports.