About this example
In single-cell analysis, alluvial diagrams are a compact way to compare clusterings or annotation methods: agreement shows as straight, unbroken flows, and disagreements show as flows that split between labels.
Here the flows are colored by the middle stage (the marker-based label), which highlights where the reference-based method assigns a different cell type.
The data
| Cluster | Marker-based | Reference-based | Cells |
|---|---|---|---|
| C1 | T cell | T cell | 1840 |
| C1 | T cell | NK cell | 210 |
| C2 | B cell | B cell | 1320 |
| C3 | Monocyte | Monocyte | 1560 |
| C3 | Monocyte | Dendritic cell | 140 |
| C4 | NK cell | NK cell | 610 |
| C4 | NK cell | T cell | 95 |
| C5 | Dendritic cell | Dendritic cell | 180 |
| C5 | Monocyte | Dendritic cell | 60 |
| C6 | Unassigned | Platelet | 120 |
| C6 | Unassigned | Unassigned | 45 |
Open the example, replace the data with your own, and export the figure as SVG, PDF or a 600 dpi PNG.