cor_to_call_topn: get top calls for each cluster

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

get top calls for each cluster

Description

get top calls for each cluster

Usage

cor_to_call_topn(
  cor_mat,
  metadata = NULL,
  col = "cluster",
  collapse_to_cluster = FALSE,
  threshold = 0,
  topn = 2
)

Arguments

cor_mat	input similarity matrix
metadata	input metadata with tsne or umap coordinates and cluster ids
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
topn	number of calls for each cluster

Value

dataframe of cluster, new potential ident, and r info

Examples

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

cor_to_call_topn(
    cor_mat = res,
    metadata = pbmc_meta,
    col = "classified",
    collapse_to_cluster = FALSE,
    threshold = 0.5
)

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