get_reduced_dimensions_UMAP_bulk {tidybulk}R Documentation

Get UMAP

Description

Get UMAP

Usage

get_reduced_dimensions_UMAP_bulk(
  .data,
  .element = NULL,
  .feature = NULL,
  .abundance = NULL,
  .dims = 2,
  top = 500,
  of_samples = TRUE,
  log_transform = TRUE,
  scale = TRUE,
  calculate_for_pca_dimensions = 20,
  ...
)

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)

calculate_for_pca_dimensions

An integer of length one. The number of PCA dimensions to based the UMAP calculatio on. If NULL all variable features are considered

...

Further parameters passed to the function uwot

Value

A tibble with additional columns


[Package tidybulk version 1.6.1 Index]