cor_to_call_rank: get ranked calls for each cluster

In NCBI-Hackathons/clustifyR: Classifier for Single-cell RNA-seq Using Cell Clusters

get ranked calls for each cluster

Description

get ranked calls for each cluster

Usage

cor_to_call_rank(
  cor_mat,
  metadata = NULL,
  cluster_col = "cluster",
  collapse_to_cluster = FALSE,
  threshold = 0,
  rename_prefix = NULL,
  top_n = NULL
)

Arguments

cor_mat	input similarity matrix
metadata	input metadata with tsne or umap coordinates and cluster ids
cluster_col	metadata column, can be cluster or cellid
collapse_to_cluster	if a column name is provided, takes the most frequent call of entire cluster to color in plot
threshold	minimum correlation coefficent cutoff for calling clusters
rename_prefix	prefix to add to type and r column names
top_n	the number of ranks to keep, the rest will be set to 100

Value

dataframe of cluster, new ident, and r info

Examples

res <- clustify(
    input = pbmc_matrix_small,
    metadata = pbmc_meta,
    cluster_col = "classified",
    ref_mat = cbmc_ref
)

cor_to_call_rank(res, threshold = "auto")

NCBI-Hackathons/clustifyR documentation built on Aug. 31, 2024, 5:35 a.m.