get_reduced_dimensions_MDS_bulk {tidybulk}R Documentation

Get dimensionality information to a tibble using MDS

Description

Get dimensionality information to a tibble using MDS

Usage

get_reduced_dimensions_MDS_bulk(
  .data,
  .element = NULL,
  .feature = NULL,
  .abundance = NULL,
  .dims = 2,
  top = 500,
  of_samples = TRUE,
  log_transform = TRUE
)

Arguments

.data

A tibble

.element

A column symbol. The column that is used to calculate distance (i.e., normally samples)

.feature

A column symbol. The column that is represents entities to cluster (i.e., normally genes)

.abundance

A column symbol with the value the clustering is based on (e.g., 'count')

.dims

A integer vector corresponding to principal components of interest (e.g., 1:6)

top

An integer. How many top genes to select

of_samples

A boolean

log_transform

A boolean, whether the value should be log-transformed (e.g., TRUE for RNA sequencing data)

Value

A tibble with additional columns


[Package tidybulk version 1.2.1 Index]