Coralysis integration function

Usage

Coralysis_integrate(
  srt_merge = NULL,
  batch = NULL,
  append = TRUE,
  srt_list = NULL,
  assay = NULL,
  do_normalization = NULL,
  normalization_method = "LogNormalize",
  do_HVF_finding = TRUE,
  HVF_source = "separate",
  HVF_method = "vst",
  nHVF = 2000,
  HVF_min_intersection = 1,
  HVF = NULL,
  coralysis_dims_use = NULL,
  nonlinear_reduction = "umap",
  nonlinear_reduction_dims = c(2, 3),
  nonlinear_reduction_params = list(),
  force_nonlinear_reduction = TRUE,
  neighbor_metric = "euclidean",
  neighbor_k = 20L,
  cluster_algorithm = "louvain",
  cluster_resolution = 0.6,
  cores = NULL,
  PrepareData_params = list(),
  RunParallelDivisiveICP_params = list(),
  RunPCA_params = list(),
  verbose = TRUE,
  seed = 11
)

Arguments

srt_merge: A merged `Seurat` object that includes the batch information.
batch: Batch variable name.
append: Append integrated results to srt_merge.
srt_list: A list of Seurat objects to be checked and preprocessed.
assay: Assay to use. NULL uses the default assay.
do_normalization: Whether data normalization should be performed.
normalization_method: The normalization method to be used. Possible values are "LogNormalize", "SCT", "TFIDF", and "scran".
do_HVF_finding, HVF_method, nHVF, HVF: Highly variable features. HVF_method is "vst", "mvp", "disp", or "scran".
HVF_source: The source of highly variable features. Possible values are "global" and "separate".
HVF_min_intersection: The feature needs to be present in batches for a minimum number of times in order to be considered as highly variable.
coralysis_dims_use: Dimensions returned by Coralysis PCA that will be utilized for downstream cell cluster finding and nonlinear reduction. If `NULL`, all available Coralysis PCA dimensions will be used by default.
nonlinear_reduction, nonlinear_reduction_dims, nonlinear_reduction_params, force_nonlinear_reduction: Nonlinear reduction ("umap", "umap-naive", "tsne", "dm", "phate", "pacmap", "trimap", "largevis", "fr").
neighbor_metric, neighbor_k: Neighbor graph ("euclidean", "cosine", "manhattan", "hamming").
cluster_algorithm, cluster_resolution: Clustering ("louvain", "slm", "leiden"). Larger cluster_resolution yields fewer clusters.
cores: Number of threads passed to [Coralysis::RunParallelDivisiveICP].
PrepareData_params: A list of parameters for [Coralysis::PrepareData].
RunParallelDivisiveICP_params: A list of parameters for [Coralysis::RunParallelDivisiveICP].
RunPCA_params: A list of parameters for [Coralysis::RunPCA].
verbose: Whether to print the message. Default is TRUE.
seed: Random seed.