sortRows: sortRows

In plger/sechm: sechm: Complex Heatmaps from a SummarizedExperiment

sortRows

Description

sortRows

Usage

sortRows(
  x,
  z = FALSE,
  toporder = NULL,
  na.rm = FALSE,
  method = "MDS_angle",
  toporder.meth = "before"
)

Arguments

x	A numeric matrix or data.frame.
z	Whether to scale rows for the purpose of calculating order.
toporder	Optional verctor of categories (length=nrow(x)) on which to supra-order when sorting rows.
na.rm	Whether to remove missing values and invariant rows.
method	Seriation method; 'MDS_angle' (default) or 'R2E' recommended.
toporder.meth	Whether to perform higher-order sorting 'before' (default) or 'after' the lower-order sorting.

Value

A reordered matrix or data.frame.

Examples

# random data
m <- matrix( round(rnorm(100,mean=10, sd=2)), nrow=10,
             dimnames=list(LETTERS[1:10], letters[11:20]) )
m
sortRows(m)

plger/sechm documentation built on June 16, 2024, 7:53 a.m.