run.diffusion.map | R Documentation |
This function takes an object of class scSeqR and runs PHATE on PCA data.
run.diffusion.map(x = NULL, dims = 1:10, method = "phate", ndim = 3, k = 5, alpha = 40, n.landmark = 2000, gamma = 1, t = "auto", knn.dist.method = "euclidean", init = NULL, mds.method = "metric", mds.dist.method = "euclidean", t.max = 100, npca = 100, plot.optimal.t = FALSE, verbose = 1, n.jobs = 1, seed = NULL, potential.method = NULL, use.alpha = NULL, n.svd = NULL, pca.method = NULL, g.kernel = NULL, diff.op = NULL, landmark.transitions = NULL, diff.op.t = NULL, dist.method = NULL)
x |
An object of class scSeqR. |
dims |
PC dimentions to be used for UMAP analysis. |
An object of class scSeqR.
## Not run: my.obj <- run.diffusion.map(my.obj, dims = 1:10, method = "phate") ## End(Not run)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.