Description Usage Arguments Details Value See Also Examples
View source: R/diffusion-map.R
URD uses the R package destiny to calculate a diffusion map.
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object |
An URD object |
genes.use |
(Character vector) Genes to use (default is variable genes, NULL uses all genes) |
cells.use |
(Character vector) Cells to use (default is NULL, which uses all cells) |
knn |
(Numeric) Number of nearest neighbors to use (NULL takes a guess) |
sigma.use |
(NULL, numeric, or "local") Kernel width to use for the diffusion map (NULL uses destiny's global auto-detection procedure, and "local" determines a sigma for each cell based on the distance to its nearest neighbors.) |
n_local |
(Numeric) If |
distance |
(Character) Distance metric to use for determining transition probabilities. |
density.norm |
(Logical) If TRUE, use density normalization |
dcs.store |
(Numeric) How many diffusion components to store |
verbose |
(Logical) Report determined values for auto-detected parameters? |
The diffusion map
is stored in the @dm
slot of the URD object, and the transition probabilities
(@dm@transitions
) are used extensively downstream in URD's pipeline.
Important parameters to vary while choosing a diffusion map to use are the number
of nearest neighbors considered (the square root of the number of cells
is a good starting point, or NULL
will trigger destiny to try to determine
a good starting point), and the sigma of the Gaussian used to transform cells'
distance.
An URD object with the diffusion map stored in @dm
.
DiffusionMap
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