RunSPCA | R Documentation |
Run a supervised PCA (SPCA) dimensionality reduction supervised by a cell-cell kernel. SPCA is used to capture a linear transformation which maximizes its dependency to the given cell-cell kernel. We use SNN graph as the kernel to supervise the linear matrix factorization.
RunSPCA(object, ...)
## Default S3 method:
RunSPCA(
object,
assay = NULL,
npcs = 50,
reduction.key = "SPC_",
graph = NULL,
verbose = FALSE,
seed.use = 42,
...
)
## S3 method for class 'Assay'
RunSPCA(
object,
assay = NULL,
features = NULL,
npcs = 50,
reduction.key = "SPC_",
graph = NULL,
verbose = TRUE,
seed.use = 42,
...
)
## S3 method for class 'Assay5'
RunSPCA(
object,
assay = NULL,
features = NULL,
npcs = 50,
reduction.key = "SPC_",
graph = NULL,
verbose = TRUE,
seed.use = 42,
layer = "scale.data",
...
)
## S3 method for class 'Seurat'
RunSPCA(
object,
assay = NULL,
features = NULL,
npcs = 50,
reduction.name = "spca",
reduction.key = "SPC_",
graph = NULL,
verbose = TRUE,
seed.use = 42,
...
)
object |
An object |
... |
Arguments passed to other methods and IRLBA |
assay |
Name of Assay SPCA is being run on |
npcs |
Total Number of SPCs to compute and store (50 by default) |
reduction.key |
dimensional reduction key, specifies the string before the number for the dimension names. SPC by default |
graph |
Graph used supervised by SPCA |
verbose |
Print the top genes associated with high/low loadings for the SPCs |
seed.use |
Set a random seed. By default, sets the seed to 42. Setting NULL will not set a seed. |
features |
Features to compute SPCA on. If features=NULL, SPCA will be run using the variable features for the Assay. |
layer |
Layer to run SPCA on |
reduction.name |
dimensional reduction name, spca by default |
Returns Seurat object with the SPCA calculation stored in the reductions slot
Barshan E, Ghodsi A, Azimifar Z, Jahromi MZ. Supervised principal component analysis: Visualization, classification and regression on subspaces and submanifolds. Pattern Recognition. 2011 Jul 1;44(7):1357-71. https://www.sciencedirect.com/science/article/pii/S0031320310005819?casa_token=AZMFg5OtPnAAAAAA:_Udu7GJ7G2ed1-XSmr-3IGSISUwcHfMpNtCj-qacXH5SBC4nwzVid36GXI3r8XG8dK5WOQui;
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