umapFromDistane: umapFromDistane.Seurat

In WilsonImmunologyLab/LinQView: Integrate information from both transcriptome and cell surface protein signals to better identify cell heterogeneity

Description

Run UMAP to project single cells into 2D space using cell-cell pairwise distances

Usage

## S3 method for class 'Seurat'
umapFromDistane(
  object,
  assay = "All",
  seed = 42,
  method = "umap-learn",
  n.neighbors = 15,
  n.components = 2,
  metric = "euclidean",
  verbose = FALSE,
  n.epochs = 200,
  min.dist = 0.1,
  spread = 1,
  set.op.mix.ratio = 1,
  local.connectivity = 1L,
  negative.sample.rate = 5L
)

## Default S3 method:
umapFromDistane(
  object,
  seed = 42,
  method = "umap-learn",
  n.neighbors = 15,
  n.components = 2,
  metric = "euclidean",
  verbose = TRUE,
  n.epochs = 200,
  min.dist = 0.1,
  spread = 1,
  set.op.mix.ratio = 1,
  local.connectivity = 1L,
  negative.sample.rate = 5L
)

umapFromDistane(object, ...)

Arguments

object	(For Seurat) Seurat object
assay	(For Seurat) run UMAP for which assay, choose from RNA, ADT, Joint or All
seed	see number. default is 42
method	could be "naive" or "umap-learn"
n.neighbors	integer; number of nearest neighbors
n.components	integer; dimension of target (output) space
metric	character or function; determines how distances between data points are computed. When using a string, available metrics are: euclidean, manhattan. Other available generalized metrics are: cosine, pearson, pearson2. Note the triangle inequality may not be satisfied by some generalized metrics, hence knn search may not be optimal. When using metric.function as a function, the signature must be function(matrix, origin, target) and should compute a distance between the origin column and the target columns
verbose	logical or integer; determines whether to show progress messages
n.epochs	integer; number of iterations performed during layout optimization
min.dist	numeric; determines how close points appear in the final layout
spread	numeric; used during automatic estimation of a/b parameters.
set.op.mix.ratio	numeric in range [0,1]; determines who the knn-graph is used to create a fuzzy simplicial graph
local.connectivity	numeric; used during construction of fuzzy simplicial set
negative.sample.rate	integer; determines how many non-neighbor points are used per point and per iteration during layout optimization

WilsonImmunologyLab/LinQView documentation built on Jan. 3, 2022, 10 p.m.