cluster_elements-methods: Get clusters of elements (e.g., samples or transcripts)

In stemangiola/ttBulk: Brings transcriptomics to the tidyverse

Get clusters of elements (e.g., samples or transcripts)

Description

cluster_elements() takes as input A 'tbl' (with at least three columns for sample, feature and transcript abundance) or 'SummarizedExperiment' (more convenient if abstracted to tibble with library(tidySummarizedExperiment)) and identify clusters in the data.

Usage

cluster_elements(
  .data,
  .element = NULL,
  .feature = NULL,
  .abundance = NULL,
  method,
  of_samples = TRUE,
  transform = log1p,
  action = "add",
  ...,
  log_transform = NULL
)

## S4 method for signature 'spec_tbl_df'
cluster_elements(
  .data,
  .element = NULL,
  .feature = NULL,
  .abundance = NULL,
  method,
  of_samples = TRUE,
  transform = log1p,
  action = "add",
  ...,
  log_transform = NULL
)

## S4 method for signature 'tbl_df'
cluster_elements(
  .data,
  .element = NULL,
  .feature = NULL,
  .abundance = NULL,
  method,
  of_samples = TRUE,
  transform = log1p,
  action = "add",
  ...,
  log_transform = NULL
)

## S4 method for signature 'tidybulk'
cluster_elements(
  .data,
  .element = NULL,
  .feature = NULL,
  .abundance = NULL,
  method,
  of_samples = TRUE,
  transform = log1p,
  action = "add",
  ...,
  log_transform = NULL
)

## S4 method for signature 'SummarizedExperiment'
cluster_elements(
  .data,
  .element = NULL,
  .feature = NULL,
  .abundance = NULL,
  method,
  of_samples = TRUE,
  transform = log1p,
  action = "add",
  ...,
  log_transform = NULL
)

## S4 method for signature 'RangedSummarizedExperiment'
cluster_elements(
  .data,
  .element = NULL,
  .feature = NULL,
  .abundance = NULL,
  method,
  of_samples = TRUE,
  transform = log1p,
  action = "add",
  ...,
  log_transform = NULL
)

Arguments

.data	A 'tbl' (with at least three columns for sample, feature and transcript abundance) or 'SummarizedExperiment' (more convenient if abstracted to tibble with library(tidySummarizedExperiment))
.element	The name of the element column (normally samples).
.feature	The name of the feature column (normally transcripts/genes)
.abundance	The name of the column including the numerical value the clustering is based on (normally transcript abundance)
method	A character string. The cluster algorithm to use, at the moment k-means is the only algorithm included.
of_samples	A boolean. In case the input is a tidybulk object, it indicates Whether the element column will be sample or transcript column
transform	A function that will tranform the counts, by default it is log1p for RNA sequencing data, but for avoinding tranformation you can use identity
action	A character string. Whether to join the new information to the input tbl (add), or just get the non-redundant tbl with the new information (get).
...	Further parameters passed to the function kmeans
log_transform	DEPRECATED - A boolean, whether the value should be log-transformed (e.g., TRUE for RNA sequencing data)

Details

'r lifecycle::badge("maturing")'

identifies clusters in the data, normally of samples. This function returns a tibble with additional columns for the cluster annotation. At the moment only k-means (DOI: 10.2307/2346830) and SNN clustering (DOI:10.1016/j.cell.2019.05.031) is supported, the plan is to introduce more clustering methods.

Underlying method for kmeans do.call(kmeans(.data, iter.max = 1000, ...)

Underlying method for SNN .data Seurat::CreateSeuratObject() Seurat::ScaleData(display.progress = TRUE,num.cores = 4, do.par = TRUE) Seurat::FindVariableFeatures(selection.method = "vst") Seurat::RunPCA(npcs = 30) Seurat::FindNeighbors() Seurat::FindClusters(method = "igraph", ...)

Value

A tbl object with additional columns with cluster labels

A tbl object with additional columns with cluster labels

A tbl object with additional columns with cluster labels

A tbl object with additional columns with cluster labels

A 'SummarizedExperiment' object

A 'SummarizedExperiment' object

Examples

    cluster_elements(tidybulk::se_mini,	centers = 2, method="kmeans")

stemangiola/ttBulk documentation built on Oct. 19, 2024, 1:34 p.m.