RunPHATE: Run PHATE (Potential of Heat-diffusion for Affinity-based...

In zh542370159/SCP: Single Cell Pipeline

Run PHATE (Potential of Heat-diffusion for Affinity-based Trajectory Embedding)

Description

Run PHATE (Potential of Heat-diffusion for Affinity-based Trajectory Embedding)

Usage

RunPHATE(object, ...)

## S3 method for class 'Seurat'
RunPHATE(
  object,
  reduction = "pca",
  dims = NULL,
  features = NULL,
  assay = NULL,
  slot = "data",
  n_components = 2,
  knn = 5,
  decay = 40,
  n_landmark = 2000,
  t = "auto",
  gamma = 1,
  n_pca = 100,
  knn_dist = "euclidean",
  knn_max = NULL,
  t_max = 100,
  do_cluster = FALSE,
  n_clusters = "auto",
  max_clusters = 100,
  reduction.name = "phate",
  reduction.key = "PHATE_",
  verbose = TRUE,
  seed.use = 11L,
  ...
)

## Default S3 method:
RunPHATE(
  object,
  assay = NULL,
  n_components = 2,
  knn = 5,
  decay = 40,
  n_landmark = 2000,
  t = "auto",
  gamma = 1,
  n_pca = 100,
  knn_dist = "euclidean",
  knn_max = NULL,
  t_max = 100,
  do_cluster = FALSE,
  n_clusters = "auto",
  max_clusters = 100,
  reduction.key = "PHATE_",
  verbose = TRUE,
  seed.use = 11L,
  ...
)

Arguments

object	An object. This can be a Seurat object or a matrix-like object.
...	Additional arguments to be passed to the phate.PHATE function.
reduction	A character string specifying the reduction to be used. Default is "pca".
dims	An integer vector specifying the dimensions to be used. Default is NULL.
features	A character vector specifying the features to be used. Default is NULL.
assay	A character string specifying the assay to be used. Default is NULL.
slot	A character string specifying the slot name to be used. Default is "data".
n_components	An integer specifying the number of PHATE components. Default is 2.
knn	An integer specifying the number of nearest neighbors on which to build kernel. Default is 5.
decay	An integer specifying the sets decay rate of kernel tails. Default is 40.
n_landmark	An integer specifying the number of landmarks to use in fast PHATE. Default is 2000.
t	A character string specifying the power to which the diffusion operator is powered. This sets the level of diffusion. If ‘auto’, t is selected according to the knee point in the Von Neumann Entropy of the diffusion operator. Default is "auto".
gamma	A numeric value specifying the informational distance constant between -1 and 1. gamma=1 gives the PHATE log potential, gamma=0 gives a square root potential. Default is 1.
n_pca	An integer specifying the number of principal components to use for calculating neighborhoods. For extremely large datasets, using n_pca < 20 allows neighborhoods to be calculated in roughly log(n_samples) time. Default is 100.
knn_dist	A character string specifying the distance metric for k-nearest neighbors. Recommended values: "euclidean, "cosine, "precomputed". Default is "euclidean".
knn_max	An integer specifying the maximum number of neighbors for which alpha decaying kernel is computed for each point. For very large datasets, setting knn_max to a small multiple of knn can speed up computation significantly. Default is NULL.
t_max	An integer specifying the maximum t to test. Default is 100.
do_cluster	A logical value indicating whether to perform clustering on the PHATE embeddings. Default is FALSE.
n_clusters	An integer specifying the number of clusters to be identified. Default is "auto".
max_clusters	An integer specifying the maximum number of clusters to test. Default is 100.
reduction.name	A character string specifying the name of the reduction to be stored in the Seurat object. Default is "phate".
reduction.key	A character string specifying the prefix for the column names of the PHATE embeddings. Default is "PHATE_".
verbose	A logical value indicating whether to print verbose output. Default is TRUE.
seed.use	An integer specifying the random seed to be used. Default is 11.

Examples

pancreas_sub <- Seurat::FindVariableFeatures(pancreas_sub)
pancreas_sub <- RunPHATE(object = pancreas_sub, features = Seurat::VariableFeatures(pancreas_sub))
CellDimPlot(pancreas_sub, group.by = "CellType", reduction = "phate")

zh542370159/SCP documentation built on Nov. 22, 2023, 2:34 a.m.