AddAdjList: Add adjacency matrix list for a PRECASTObj object

In PRECAST: Embedding and Clustering with Alignment for Spatial Datasets

Add adjacency matrix list for a PRECASTObj object

Description

Add adjacency matrix list for a PRECASTObj object to prepare for PRECAST model fitting.

Usage

  AddAdjList(PRECASTObj, type="fixed_distance", platform="Visium", ...)

Arguments

PRECASTObj	a PRECASTObj object created by CreatePRECASTObject.
type	an optional string, specify which type of neighbors' definition. Here we provide two definition: one is "fixed_distance", the other is "fixed_number".
platform	a string, specify the platform of the provided data, default as "Visium". There are more platforms to be chosen, including "Visuim", "ST" and "Other_SRT" ("Other_SRT" represents the other SRT platforms except for 'Visium' and 'ST'), which means there are spatial coordinates information in the metadata of PRECASTObj. The platform helps to calculate the adjacency matrix by defining the neighborhoods when type="fixed_distance" is chosen.
...	other arguments to be passed to getAdj, getAdj_auto and getAdj_fixedNumber funciton.

Details

When the type = "fixed_distance", then the spots within the Euclidean distance cutoffs from one spot are regarded as the neighbors of this spot. When the type = "fixed_number", the K-nearest spots are regarded as the neighbors of each spot.

Value

Return a revised PRECASTObj object by adding the adjacency matrix list.

Note

nothing

Author(s)

Wei Liu

See Also

AddParSetting.

PRECAST documentation built on May 29, 2024, 3 a.m.