get_reduced_dimensions_UMAP_bulk_SE: Get UMAP

In stemangiola/tidybulk: Brings transcriptomics to the tidyverse

Get UMAP

Description

Get UMAP

Usage

get_reduced_dimensions_UMAP_bulk_SE(
  .data,
  .dims = 2,
  top = 500,
  of_samples = TRUE,
  transform = log1p,
  scale = NULL,
  calculate_for_pca_dimensions = min(20, top),
  ...
)

Arguments

.data	A tibble
.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
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
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::tumap
.abundance	A column symbol with the value the clustering is based on (e.g., 'count')
.feature	A column symbol. The column that is represents entities to cluster (i.e., normally genes)
.element	A column symbol. The column that is used to calculate distance (i.e., normally samples)

Value

A tibble with additional columns

stemangiola/tidybulk documentation built on Oct. 23, 2024, 8 a.m.