This section has various HowTo tutorials that aim to spotlight some of the ways in which Giotto can be used.
- Working With The Giotto Class
- How To Subset Giotto Objects
- 1. The Visium 10X Whole Brain
- 2. Show Only A Subset of Clusters
- 3. Show Only A Subset of Clusters (excluding not selected cells)
- 4. Create Spatial Plots
- 5. Create Dimension Plots
- 6. Create A New Giotto Object By Subsetting Selected Clusters
- 7. Create A New Giotto Object By Subsetting Spatial Coordinates/Locations
- How To Visualize And Save Plots in Giotto
- How to Test and Store Multiple Parameters or Analyses
- Different Ways to Visualize Spatial Data
- 1. Task/Analysis Specific Functions
- 2. Functions that use the Spatial Coordinates of a Cell/Spot
- 3. Functions that use the Dimension Reduction Coordinates of a Cell/Spot
- 4. Functions for co-visualization that combine spat (2) and dim (3)
- 5. Both in 2D and 3D
- 6. Ways to Save Plots
- 7. Hypothetical Example
- How To Add And Work With Images in Giotto
- How To Visualize Spatial Data with Voronoi Plots
Giotto provides a lot of analyses, visualizations and other options to facilitate your spatial dataset analysis. We are working on providing easy-to-understand examples or tutorials, but if anything is not clear or if there is something you would like to see in particular, then do not hesitate to contact us.
In addition to our HowTos we have also created a way for users to test out Giotto via Docker, Binder, or Terra. (see Try Giotto for more information).