This function computes low-dimensional cell embeddings from a gene-by-cell matrix. The method initializes cell embeddings using approximate PCA and refines them through a linear factor model nested a intrinsical conditional autoregressive model.
cellembedding_matrix(X, adjm, q = 50, reduction.name = "caesar", ...)A gene-by-cell matrix (e.g., the `data` slot from a Seurat object) that serves as the input data for dimensional reduction.
A spatial adjacency matrix representing the relationships between cells or spots in spatial transcriptomic data.
An integer specifying the number of dimensions to reduce to. Default is 50.
A character string specifying the name of the dimensional reduction method. Default is 'caesar'.
Additional parameters passed to `ProFAST::FAST_run`.
A matrix containing the computed cell embeddings. The number of rows corresponds to the number of cells, and the number of columns corresponds to the specified number of dimensions (`q`).
FAST_run for the main FAST dimensionality reduction algorithm.
data(toydata)
seu <- toydata$seu
pos <- toydata$pos
adjm <- ProFAST::AddAdj(as.matrix(pos), radius.upper = 200)
#> The spatial cooridnates are 2 dimensions
#> Find the adjacency matrix by bisection method...
#> Current radius is 100.5
#> Median of neighborhoods is 0
#> Current radius is 50.75
#> Median of neighborhoods is 17
#> Current radius is 50.75
#> Median of neighborhoods is 4
X <- Seurat::GetAssayData(object = seu, slot = "data", assay = "RNA")
cellembedding <- cellembedding_matrix(
X = X,
adjm = adjm
)
#> Finish variable intialization
#> Satrt ICM and E-step!
#> Finish ICM and E-step!
#> iter = 2, loglik= -597713.932765, dloglik=0.999722
#> Satrt ICM and E-step!
#> Finish ICM and E-step!
#> iter = 3, loglik= -572981.633443, dloglik=0.041378
#> Satrt ICM and E-step!
#> Finish ICM and E-step!
#> iter = 4, loglik= -568540.760390, dloglik=0.007750
#> Satrt ICM and E-step!
#> Finish ICM and E-step!
#> iter = 5, loglik= -565577.203830, dloglik=0.005213
#> Satrt ICM and E-step!
#> Finish ICM and E-step!
#> iter = 6, loglik= -563808.620547, dloglik=0.003127
#> Satrt ICM and E-step!
#> Finish ICM and E-step!
#> iter = 7, loglik= -562445.787433, dloglik=0.002417
#> Satrt ICM and E-step!
#> Finish ICM and E-step!
#> iter = 8, loglik= -561479.215323, dloglik=0.001719
#> Satrt ICM and E-step!
#> Finish ICM and E-step!
#> iter = 9, loglik= -560721.438599, dloglik=0.001350
#> Satrt ICM and E-step!
#> Finish ICM and E-step!
#> iter = 10, loglik= -560111.513183, dloglik=0.001088
#> Satrt ICM and E-step!
#> Finish ICM and E-step!
#> iter = 11, loglik= -559583.251469, dloglik=0.000943
#> Satrt ICM and E-step!
#> Finish ICM and E-step!
#> iter = 12, loglik= -559112.175571, dloglik=0.000842
#> Satrt ICM and E-step!
#> Finish ICM and E-step!
#> iter = 13, loglik= -558672.733365, dloglik=0.000786
#> Satrt ICM and E-step!
#> Finish ICM and E-step!
#> iter = 14, loglik= -558253.012300, dloglik=0.000751
#> Satrt ICM and E-step!
#> Finish ICM and E-step!
#> iter = 15, loglik= -557843.814583, dloglik=0.000733
#> Satrt ICM and E-step!
#> Finish ICM and E-step!
#> iter = 16, loglik= -557444.260607, dloglik=0.000716
#> Satrt ICM and E-step!
#> Finish ICM and E-step!
#> iter = 17, loglik= -557056.241772, dloglik=0.000696
#> Satrt ICM and E-step!
#> Finish ICM and E-step!
#> iter = 18, loglik= -556685.140174, dloglik=0.000666
#> Satrt ICM and E-step!
#> Finish ICM and E-step!
#> iter = 19, loglik= -556336.124902, dloglik=0.000627
#> Satrt ICM and E-step!
#> Finish ICM and E-step!
#> iter = 20, loglik= -556014.108493, dloglik=0.000579
#> Satrt ICM and E-step!
#> Finish ICM and E-step!
#> iter = 21, loglik= -555721.816223, dloglik=0.000526
#> Satrt ICM and E-step!
#> Finish ICM and E-step!
#> iter = 22, loglik= -555459.782139, dloglik=0.000472
#> Satrt ICM and E-step!
#> Finish ICM and E-step!
#> iter = 23, loglik= -555225.898188, dloglik=0.000421
#> Satrt ICM and E-step!
#> Finish ICM and E-step!
#> iter = 24, loglik= -555016.558071, dloglik=0.000377
#> Satrt ICM and E-step!
#> Finish ICM and E-step!
#> iter = 25, loglik= -554827.351177, dloglik=0.000341
print(cellembedding[1:3, 1:3])
#> caesar_1 caesar_2 caesar_3
#> 24387 -5.975308 8.496165 6.2566729
#> 4049 -7.061217 -3.932074 -0.6449155
#> 11570 -8.719022 -6.024967 -1.9306196