run.diffusion.map: Run PHATE on PCA data (PHATE - Potential of Heat-Diffusion...

In rezakj/scSeqR: scSeqR; a toolkit to analyze single cell sequencing data types (i.e scRNA-seq) and large numeric matrix files.

Run PHATE on PCA data (PHATE - Potential of Heat-Diffusion for Affinity-Based Transition Embedding)

Description

This function takes an object of class scSeqR and runs PHATE on PCA data.

Usage

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)

Arguments

x	An object of class scSeqR.
dims	PC dimentions to be used for UMAP analysis.

Value

An object of class scSeqR.

Examples

## Not run: 
my.obj <- run.diffusion.map(my.obj, dims = 1:10, method = "phate")

## End(Not run)

rezakj/scSeqR documentation built on March 28, 2022, 12:17 p.m.