In pascalcroteau/matrixset: Creating, Manipulating and Annotating Matrix Ensemble

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)

matrixset

A matrixset is a container of matrices (both matrix and types from Matrix package), each having the same number of rows and columns and the same dimnames. Moreover, each dimname must uniquely identify elements.

While there is minimal support for NULL dimnames (and that is bound to change at some point in the future), it is strongly recommended to provide meaningful dimnames. One of the main reason for this is that annotation is impossible with NULL dimnames.

In addition, as alluded above, a matrixset can store independent row and column annotations. This meta information is stored, and available, in the form of data frames - one for row information and one for column. The annotation names are referred to as traits.

This latter feature makes matrixset especially attractive even if it stores only a single matrix, because several methods have been developped to manipulate matrixsets, accounting for annotations.

Why a matrixset?

Many problems that matrixset can tackle could be solved via a data.frame and more specifically using the tidyverse suite.

Three reasons for which you may want to use a matrixset instead are:

object size. The data.frame needed to store the same information as a matrixset can be significantly bigger
You can store sparse matrices and other special matrices of package Matrix. This is one of very few ways (maybe even the only way) to annotate special matrices. In addition, dealing with special matrices make the object size argument even more striking when comparing to the data frame strategy.
You actually need a matrix format, for example for running a PCA.

Installation

The easiest way to install matrixset is from CRAN:

install.packages("matrixset")

Or you can install the development version of matrixset from GitHub with:

# install.packages("devtools")
devtools::install_github("pascalcroteau/matrixset")

Example

In addition to store multiple matrices that share the same attributes, a matrixset object's strength is it's annotation feature. You create an object from existing matrices and annotation data.frame.

library(MASS)
library(tidyverse)
animals <- as.matrix(Animals)
head(animals)


animal_info <- MASS::Animals %>% 
  rownames_to_column("Animal") %>% 
  mutate(is_extinct = case_when(Animal %in% c("Dipliodocus", "Triceratops", "Brachiosaurus") ~ TRUE,
                                TRUE ~ FALSE),
         class = case_when(Animal %in% c("Mountain beaver", "Guinea pig", "Golden hamster", "Mouse", "Rabbit", "Rat") ~ "Rodent",
                           Animal %in% c("Potar monkey", "Gorilla", "Human", "Rhesus monkey", "Chimpanzee") ~ "Primate",
                           Animal %in% c("Cow", "Goat", "Giraffe", "Sheep") ~ "Ruminant",
                           Animal %in% c("Asian elephant", "African elephant") ~ "Elephantidae",
                           Animal %in% c("Grey wolf") ~ "Canine",
                           Animal %in% c("Cat", "Jaguar") ~ "Feline",
                           Animal %in% c("Donkey", "Horse") ~ "Equidae",
                           Animal == "Pig" ~ "Sus",
                           Animal == "Mole" ~ "Talpidae",
                           Animal == "Kangaroo" ~ "Macropodidae",
                           TRUE ~ "Dinosaurs")) %>% 
  select(-body, -brain)
animal_info

You can create the object and then do some operations.

library(matrixset)
animals_ms <- matrixset(msr = animals, row_info = animal_info, row_key = "Animal")
animals_ms %>% 
    apply_row_dfl(rg = ~ range(.i),
                  qt = ~ quantile(.i, probs = c(.25, .75)))   


animals_ms %>% 
    row_group_by(class) %>% 
    apply_column_dfl(avr = mean)