createFromSeurat: Creates a 'TreeViz' object from 'Seurat'

In jkanche/TreeSE: R/Bioconductor package to interactively explore and visualize single cell RNA-seq datasets with hierarhical annotations

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"))

jkanche/TreeSE documentation built on Oct. 1, 2021, 8:31 p.m.