A collection of notebooks to recreate some of the visualizations as published in my scientific papers.

Visualizations - hierarchy

HierTree: An example for plotting a hierarchical tree (not dendrogram!) based on result from hierarchical clustering.



Sunburst:



Visualizations - sc/snRNA-seq

UMAP-Constellation: Creating a UMAP and constellation from small single cell RNA-seq dataset



3D UMAP: Creating a 3D UMAP from small single cell RNA-seq dataset



Node dodge app : Creating a 3D UMAP from small single cell RNA-seq dataset



Visualizations - spatialTX

SpatialTx with CCF outlines:



3D SpatialTx:



Visualizations - CCF

Flatmaps:



ABA - ISH:



ABA - svg:



Visualizations - random