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