Description Usage Arguments Value Examples
View source: R/mcaAndReduction.R
Run DiffusionMap on MCA cell and feature coordinates
1 2 3 4 5 6 7 8 9 10 | RunMCDMAP(X, reduction, features, dims, reduction.name, ...)
## S3 method for class 'Seurat'
RunMCDMAP(X, reduction = "mca", features = NULL,
dims = seq(50), reduction.name = "mcdmap", assay = DefaultAssay(X),
...)
## S3 method for class 'SingleCellExperiment'
RunMCDMAP(X, reduction = "MCA",
features = NULL, dims = seq(50), reduction.name = "MCDMAP", ...)
|
X |
Seurat or SingleCellExperiment object |
reduction |
Which dimensionality reduction to use, must be based on MCA. |
features |
Character vector of feature names to subset feature coordinates. If not specified will take all features available from specified reduction Loadings. |
dims |
A vector of integers indicating which dimensions to use with reduction embeddings and loadings for distance calculation. |
reduction.name |
name of the created dimensionlaity reduction, default set to "mca" for Seurat and "MCA" for SCE. |
... |
other arguments passed to methods or DiffusionMap |
assay |
Seurat Asssay slot name. |
Seurat or SingleCellExperiment object with MCDMAP stored in the reduction slot
1 2 | seuratPbmc <- RunMCA(seuratPbmc, nmcs = 5)
seuratPbmc <- RunMCDMAP(seuratPbmc, dims = seq(5))
|
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