createFromSeurat {scTreeViz}R Documentation

Creates a 'TreeViz' object from 'Seurat'

Description

Creates a 'TreeViz' object from 'Seurat'

Usage

createFromSeurat(
  object,
  check_metadata = FALSE,
  col_regex = "*snn*",
  columns = NULL,
  reduced_dim = c("TSNE")
)

Arguments

object

'Seurat' class containing cluster information at different resolutions

check_metadata

whether to metaData of 'Seurat' object for cluster information or not

col_regex

common regular expression shared across all columns with cluster information

columns

vector containing columns with cluster information

reduced_dim

Vector of Dimensionality reduction information provided in 'Seurat' object to be added in 'TreeViz' (if exists)

Value

'TreeViz' Object

Examples

library(Seurat)
data(pbmc_small)
pbmc <- pbmc_small
treeviz<- createFromSeurat(pbmc, check_metadata = TRUE, reduced_dim = c("pca","tsne"))

[Package scTreeViz version 0.99.11 Index]