HowTos

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
  • 1. The Giotto Class
  • 2. Giotto Slots
• 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
  • 1. Create Giotto Instructions and Giotto object
  • 2. Create Giotto Object
  • 3. Working with Giotto Instructions
  • 4. Different Ways of Saving a Plot
• How to Test and Store Multiple Parameters or Analyses
  • 1. Calculate Highly Variable Genes (2 Methods)
  • 2. Perform Multiple PCAs
  • 3. Create Multiple UMAPs
  • 4. Create Multiple Spatial Networks
  • 5. Find Spatial Genes (Multiple Methods)
• 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
  • 1. Create Giotto Object
  • 2. Align Plot
  • 3. Change Background of a Giotto or Magick Image
  • 4. Add Image From Scratch
  • 5. Example: Kidney Analysis
• How To Visualize Spatial Data with Voronoi Plots
  • 1. Analysis of the mini seqFISH+ dataset
  • 2. Example: Voronoi Plot
  • 3. Creating and Showing Neighbors
  • 4. Gene Expression and 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. for more information).