grouped_reorder: Grouped Reorder and Ungroup

In jlaffy/scalop: Single Cell Analysis Operations

Grouped Reorder and Ungroup

Description

Keep desired groups together but reorder members within each group. E.g. If cells from multiple samples are being reordered, samples can be kept together and cells reordered within. Option to also reorder the order of groups or samples, such that groups with similar average profiles are placed next to one another.

Usage

grouped_reorder(
  m,
  groups,
  interorder = FALSE,
  intraorder = TRUE,
  cor.method = "pearson",
  dist.method = "euclidean",
  cluster.method = "average",
  Names = FALSE
)

Arguments

m	matrix to be reordered
groups	groups within which reordering should take place.
interorder	if TRUE, group order itself is reordered such that groups with similar profiles are placed near one another. E.g. Samples with similar average CNA profiles. Default: FALSE
cor.method	desired correlation metric. Default: 'pearson'
dist.method	desired distance metric to be used on top of correlation matrix. Default: 'euclidean'
cluster.method	desired agglomeration method. Default: 'average'
Names	return the vector of ordered IDs instead of the reordered matrix. Default: FALSE

Value

reordered matrix (same dimensions as input) or a character vector of ordered column names if Names = T.

jlaffy/scalop documentation built on March 24, 2024, 9 a.m.