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