AddAdj: Calculate the adjacency matrix given a spatial coordinate...
In ProFAST: Probabilistic Factor Analysis for Spatially-Aware Dimension Reduction
AddAdj R Documentation
Calculate the adjacency matrix given a spatial coordinate matrix
Description
Calculate the adjacency matrix given a spatial coordinate matrix with 2-dimension or 3-dimension or more.
Usage
AddAdj(
pos,
type = "fixed_distance",
platform = c("Others", "Visium", "ST"),
neighbors = 6,
...
)
Arguments
pos
a matrix object, with columns representing the spatial coordinates that can be any diemsion, i.e., 2, 3 and >3.
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 "Others". There are more platforms to be chosen, including "Visuim", "ST" and "Others" ("Others" represents the other SRT platforms except for 'Visium' and 'ST')
The platform helps to calculate the adjacency matrix by defining the neighborhoods when type="fixed_distance" is chosen.
neighbors
an optional postive integer, specify how many neighbors used in calculation, default as 6.
...
Other arguments passed to getAdj_auto.
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 sparse matrix, representing the adjacency matrix.
References
None
See Also
None
Examples
data(CosMx_subset)
pos <- as.matrix(CosMx_subset@meta.data[,c("x", "y")])
Adj_sp <- AddAdj(pos)
ProFAST documentation built on May 29, 2024, 7:15 a.m.
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| AddAdj | R Documentation |
Calculate the adjacency matrix given a spatial coordinate matrix
Description
Calculate the adjacency matrix given a spatial coordinate matrix with 2-dimension or 3-dimension or more.
Usage
AddAdj(
pos,
type = "fixed_distance",
platform = c("Others", "Visium", "ST"),
neighbors = 6,
...
)
Arguments
pos |
a matrix object, with columns representing the spatial coordinates that can be any diemsion, i.e., 2, 3 and >3. |
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 "Others". There are more platforms to be chosen, including "Visuim", "ST" and "Others" ("Others" represents the other SRT platforms except for 'Visium' and 'ST') The platform helps to calculate the adjacency matrix by defining the neighborhoods when type="fixed_distance" is chosen. |
neighbors |
an optional postive integer, specify how many neighbors used in calculation, default as 6. |
... |
Other arguments passed to |
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 sparse matrix, representing the adjacency matrix.
References
None
See Also
None
Examples
data(CosMx_subset)
pos <- as.matrix(CosMx_subset@meta.data[,c("x", "y")])
Adj_sp <- AddAdj(pos)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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