harmony_analysis: Analysis steps for Harmony integration

In andreaskapou/SeuratPipe: Packaging common Seurat analysis tasks

Analysis steps for Harmony integration

Description

This function implements all the analysis steps for performing Harmony integration on a Seurat object. These include, 1. merge all samples in a single Seurat object (if a list of Seurat objects is provided) 2. data normalisation, 3. identification of HVGs, 4. Scaling of expression values and computing PCA, 5. running Harmony integration, 8. Generating plots.

Usage

harmony_analysis(
  seu,
  batch_id = "sample",
  npcs,
  dims.use = NULL,
  plot_dir = NULL,
  n_hvgs = 3000,
  max.iter.harmony = 50,
  seed = 1,
  fig.res = 200,
  ...
)

Arguments

seu	Seurat object (required).
batch_id	Name of batch to try and remove with data integration (required). Can also be a vector if multiple batch information are present. Should be a column name in Seurat 'meta.data'. Default is "sample". This parameter is called 'group.by.vars' in Harmony.
npcs	Number of principal components.
dims.use	Vector with PCs to use for Harmony integration, e.g. 1:50.
plot_dir	Directory to save generated plots. If NULL, plots are not saved.
n_hvgs	Number of highly variable genes (HVGs) to compute, which will be used as input to PCA.
max.iter.harmony	Maximum number of iterations for Harmony integration.
seed	Set a random seed, for reproducibility.
fig.res	Figure resolution in ppi (see 'png' function).
...	Additional named parameters passed to RunHarmony and other Seurat processing functions, such as RunPCA and ScaleData.

Value

Updated Seurat object with integrated and processed data.

Author(s)

C.A.Kapourani [e-mail]

andreaskapou/SeuratPipe documentation built on Nov. 22, 2022, 4:16 p.m.