RunPalantirDiffusionMap | R Documentation |
This is a deprecated version of the Palantir Diffusion Map function.
Please refer to the updated function, Palantir.RunDM
, for the latest features and improvements.
This older version, in addition to calculating the diffusion map (dm) and multiscale_space (ms),
also calculates t-SNE. To use the t-SNE feature, the multicore-tsne
package needs to be installed in the conda environment.
RunPalantirDiffusionMap(seu, reduction = "pca", n_components = 20)
seu |
A Seurat object. |
reduction |
A character string specifying the dimension reduction to use. Default: 'pca'. |
n_components |
An integer specifying how many dimensions to use as input. Default: 20. |
A Seurat object with added dm, ms, and t-SNE embeddings.
Palantir.RunDM
for the updated version of this function.
## Not run:
library(Seurat)
library(SeuratExtend)
pbmc <- RunPalantirDiffusionMap(pbmc)
DimPlot(pbmc, reduction = "tsne", label = TRUE)
## End(Not run)
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