Description Usage Arguments Value
Run a diffusion map dimensionality reduction. For details about stored difussion map calculation
parameters, see PrintDiffusionParams
.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 | ## S3 method for class 'matrix'
RunDiffusion(
object,
assay = NULL,
dim.embed = 2,
q = 0.01,
reduction.key = "DMC_",
...
)
## S3 method for class 'DimReduc'
RunDiffusion(
object,
cells = NULL,
dims = 1:5,
q = 0.01,
dim.embed = 2,
reduction.key = "DMC_",
...
)
## S3 method for class 'Seurat'
RunDiffusion(
object,
assay = NULL,
cells = NULL,
dims = 1:5,
reduction = "diffusionmap",
features = NULL,
normalize.method = c("LogNormalize", "SCTransform"),
q = 0.01,
dim.embed = 2,
scale.clip = 10,
reduction.name = "diffusionmap",
reduction.key = "DMC_",
...
)
RunDiffusion(object, ...)
|
object |
An object |
assay |
Name of Assay diffusion map is being run on |
dim.embed |
Total Number of diffusion map components (DMCs) to compute and store (2 by default) |
q |
Quantile to clip diffusion map components at. This addresses an issue where 1-2 cells will have extreme values that obscure all other points. 0.01 by default |
reduction.key |
dimensional reduction key, specifies the string before the number for the dimension names. DMC by default |
... |
Arguments passed to other methods and destiny |
cells |
Which cells to analyze (default, all cells) |
dims |
Which dimensions to use as input features. |
reduction |
Which dimensional reduction (e.g. PCA, ICA) to use for the diffusion map. Default is PCA |
features |
If set, run the diffusion map on this subset of features
(instead of running on a set of reduced dimensions). Not set (NULL) by default;
|
normalize.method |
'LogNormalize' or 'SCTransform'. If NULL, set 'LogNormalize' by default |
scale.clip |
Max/min value for scaled data. Default is 10 |
reduction.name |
dimensional reduction name, specifies the position in the object$dr list. diffusionmap by default |
Returns Seurat object with the diffusion map calculation stored in the reductions slot
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