createFromSCE: Creates a 'TreeViz" object from 'SingleCellExperiment'....

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

Description

Creates a 'TreeViz“ object from 'SingleCellExperiment'. Generates clusters based on Walktrap algorithm if no default is provided

Usage

createFromSCE(
  object,
  check_coldata = FALSE,
  col_regex = NULL,
  columns = NULL,
  reduced_dim = c("TSNE")
)

Arguments

object	'SingleCellExperiment' object to be visualized
check_coldata	whether to colData of 'SingeCellExperiment' 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 'SingeCellExperiment' object to be added in 'TreeViz' (if exists)

Value

'TreeViz' Object

Examples

library(SingleCellExperiment)
library(scater)
sce <- mockSCE()
sce <- logNormCounts(sce)
sce <- runTSNE(sce)
sce <- runUMAP(sce)
set.seed(1000)
for (i in  seq_len(5)) {
clust.kmeans <- kmeans(reducedDim(sce, "TSNE"), centers = i)
sce[[paste0("clust", i)]] <- factor(clust.kmeans$cluster)
}
treeviz <-createFromSCE(sce, check_coldata = TRUE, col_regex = "clust", reduced_dim = c("TSNE", "UMAP"))

HCBravoLab/TreeSE documentation built on Sept. 27, 2021, 4:19 p.m.