extract_values: extract_values Extract values from PCA, UMAP, and tSNE

In jcooperdevlin/JoesFlow: Joes Flow simplified analysis for single cell modality data

extract_values Extract values from PCA, UMAP, and tSNE

Description

extract_values Extract values from PCA, UMAP, and tSNE

Usage

extract_values(clustered_data, ...)

## S3 method for class 'prcomp'
extract_values(clustered_data, ids, meta, grp, cluster = NULL, ...)

## S3 method for class 'matrix'
extract_values(clustered_data, ids, meta, grp, cluster = NULL, ...)

Arguments

clustered_data	Object containing clustered data (expects output from 'prcomp', 'umap', or 'tsne')
...	Other objects passed to methods of 'extract_values'
ids	Character vector of ids for each row in 'clustered_data', corresponding to labels in 'grps'
meta	Data frame containing translation from id to group
grp	Character value identifying the column of 'meta' to use for group identifier
cluster	Data frame containing sample ID and the assigned kmeans cluster, as returned by 'kmeaner()'

Value

A tibble with values for SampleID, Group, Cluster, PC/vector 1, and PC/vector 2

jcooperdevlin/JoesFlow documentation built on April 7, 2023, 12:42 p.m.