create_embedding: Create PCA embedding

In sshen82/BandNorm: BandNorm Method for single-cell Hi-C

Create PCA embedding

Description

This function allows you to obtain the PCA embedding for tSNE or UMAP plotting.

Usage

create_embedding(
  path = NULL,
  hic_df = NULL,
  chrs = paste0("chr", c(1:19, "X")),
  dim_pca = 50,
  do_harmony = FALSE,
  batch = NULL
)

Arguments

path	The path for all the normalized cells in a directory. There can be sub-directories. Using path means loading the bandnorm normalized data iteratively from the directory, so it is relatively slower than using hic_df. However, it won't eat up your memory too much, and the speed is acceptable.
hic_df	After using bandnorm, if you keep the data frame, it is possible to use this instead of "path" as input of create_embedding. If using hic_df, the speed will be faster, but is costs more memory.
chrs	Chromosomes used in the embedding. Default is chr1, ..., chr19, and chrX.
dim_pca	Dimension of PCA embedding to be outputted. Default is 50.
do_harmony	Whether to use Harmony to remove the batch effect from the embedding. Default is FALSE
batch	The batch information used for Harmony to remove the batch effect. Required if do_harmony is TRUE.

Examples

data("hic_df")
data("batch")
bandnorm_result = bandnorm(hic_df = hic_df, save = FALSE)
embedding = create_embedding(hic_df = bandnorm_result, do_harmony = TRUE, batch = batch)

sshen82/BandNorm documentation built on June 1, 2025, 6:25 p.m.