Working with the Giotto class: How to create Giotto object with precomputed results?

1. The Giotto Class

A Giotto object or gobject can be created with createGiottoObject or createGiottoVisiumObject for Visium datasets.

gobject = createGiottoObject()

gvisiumobject = createGiottoVisiumObject()

createGiottoVisiumObject expects a typical Visium 10X data folder structure or a path to the h5 file, but createGiottoObject is more flexible and can also accept precomputed results (e.g. PCA, UMAP, network, …)

2. Giotto Slots

2.1 Required Slots

The minimum requirements to make a Giotto class object are:

  • Raw_exprs: matrix with raw expression values

  • Spatial_locs: spatial coordinates for the cell (or spot) centroids. If this is not provided it will actually create dummy coordinates.

2.2 Additional Matrix Slots

  • norm_expr: slot to keep matrix with normalized expression values

    • Use expression_values = ‘normalized’ to access this slot in downstream functions

  • norm_scaled_expr: slot to keep matrix with normalized and scaled expression values

    • Use expression_values = ‘scaled’ to access this slot in downstream functions

  • custom_expr: slot to keep matrix with custom values

    • Use expression_values = ‘custom’ to access this slot in downstream functions