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