sort_tomic: Sort Triple Omic

In romic: R for High-Dimensional Omic Data

Sort Triple Omic

Description

Sort a dataset's features or samples

Usage

sort_tomic(
  tomic,
  sort_type,
  sort_table,
  sort_variables = NULL,
  value_var = NULL
)

Arguments

tomic	Either a tidy_omic or triple_omic object
sort_type	hclust Arrange samples by hierarchical clustering of a provided value_var arrange Arrange samples by the factor or alphanumeric ordering of a set of sort_variables
sort_table	samples or features
sort_variables	A set of attributes in sort_table to sort with in arrange.
value_var	An abundance value to use with hclust

Details

sort_tomic supports the reordering of features or samples using either hierarchical clustering or based on the levels of other variables. Sorting occurs by turning either the feature or sample primary key into a factor whose levels reflect the sort.

Value

A tomic object where feature or sample primary keys have been turned into a factor reflecting how they are sorted.

Examples

library(dplyr)

sort_tomic(brauer_2008_triple,
  sort_type = "arrange", sort_table = "samples",
  sort_variables = c("nutrient", "DR")
) %>%
  sort_tomic(
    sort_type = "hclust",
    sort_table = "features",
    value_var = "expression"
  )

romic documentation built on Sept. 21, 2023, 9:06 a.m.