Create monocle object

Use a normalized expression matrix and, potentially, an already generated PCA / UMAP embedding, to create a Monocle object.

Usage

create_monocle_default(
  normalized_expression_matrix,
  count_matrix = NULL,
  pca_embedding = NULL,
  umap_embedding = NULL,
  metadata_df = NULL
)

Arguments

normalized_expression_matrix

The normalized expression matrix having genes on rows and cells on columns.

count_matrix

The count matrix having genes on rows and cells on columns. If NULL, the normalized_expression_matrix will be used.

pca_embedding

The PCA embedding of the expression matrix. If NULL, the pca will be created using the monocle3 package (default parameters).

umap_embedding

The UMAP embedding of the expression matrix. If NULL, the umap will be created using the monocle3 package (default parameters).

metadata_df

The metadata dataframe having the cell names as rownames. If NULL, a dataframe with a single column named identical_ident will be created.

Value

A Monocle object of the expression matrix, having the stable number of clusters identified by ClustAssess.

Examples

if (FALSE) { # \dontrun{
set.seed(2024)
# create an already-transposed artificial expression matrix
expr_matrix <- matrix(
    c(runif(20 * 10), runif(30 * 10, min = 3, max = 4)),
    nrow = 10, byrow = FALSE
)
colnames(expr_matrix) <- as.character(seq_len(ncol(expr_matrix)))
rownames(expr_matrix) <- paste("feature", seq_len(nrow(expr_matrix)))

# uncomment to create the monocle object
mon_obj <- create_monocle_default(
    normalized_expression_matrix = expr_matrix,
    pca_emb = NULL,
    umap_emb = NULL,
    metadata_df = NULL
)
} # }