createFromSCE {scTreeViz} | R Documentation

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

### 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"))

[Package scTreeViz version 1.0.0 Index]