cor_to_call_rank {clustifyr}R Documentation

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")

[Package clustifyr version 1.4.0 Index]