buildReferenceFromHarmonyObj {symphony}

Function for building a Symphony reference from a Harmony object. Useful if you would like your code to be more modular. Note that you must have saved vargenes_means_sds and PCA loadings.

Description

Function for building a Symphony reference from a Harmony object. Useful if you would like your code to be more modular. Note that you must have saved vargenes_means_sds and PCA loadings.

Usage

buildReferenceFromHarmonyObj(
  harmony_obj,
  metadata,
  vargenes_means_sds,
  pca_loadings,
  verbose = TRUE,
  do_umap = TRUE,
  save_uwot_path = NULL,
  umap_min_dist = 0.1,
  seed = 111
)

Arguments

harmony_obj

Harmony object (output from HarmonyMatrix())

metadata

Reference cell metadata (cells by attributes)

vargenes_means_sds

Variable genes in dataframe with columns named ('symbol', 'mean', 'stddev')

pca_loadings

Gene loadings from PCA (e.g. irlba(ref_exp_scaled, nv = 20)$u)

verbose

Verbose output

do_umap

Perform UMAP visualization on harmonized reference embedding

save_uwot_path

Absolute path to save the uwot model (if do_umap is TRUE)

umap_min_dist

UMAP parameter (see uwot documentation for details)

seed

Random seed

Value

Symphony reference object. Integrated embedding is stored in the $Z_corr slot. Other slots include cell-level metadata ($meta_data), variable genes means and standard deviations ($vargenes), loadings from PCA or other dimensional reduction such as CCA ($loadings), original PCA embedding ($Z_orig), reference compression terms ($cache), betas from Harmony integration ($betas), cosine-normalized soft cluster centroids ($centroids), centroids in PC space ($centroids_pc), and optional umap coordinates ($umap$embedding).