Applying Functions

In matrixset: Creating, Manipulating and Annotating Matrix Ensemble

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
library(matrixset)

library(tidyverse)
animals <- as.matrix(MASS::Animals)
log_animals <- log(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)
animals_ms <- matrixset(msr = animals, log_msr = log_animals, row_info = animal_info,
                row_key = "Animal")
animals_ms <- animals_ms %>% 
  annotate_column(unit = case_when(.colname == "body" ~ "kg",
                                   TRUE ~ "g")) 

Apply Functions to matrixset Matrices

There are two ways to apply functions to the matrices of a matrixset object. The first one is through the apply_* family, which will be covered here.

The second is through mutate_matrix(), covered in the next section.

There are 3 functions in the apply_* family:

• apply_matrix(): The functions must take a matrix as input. In base R, this is similar to simply calling fun(matrix_object).
• apply_row(): The functions must take a vector as input. The vector will be a matrix row. In base R, this is akin to apply(matrix_object, 1, fun, simplify = FALSE).
• apply_column(): The functions must take a vector as input. The vector will be a matrix column. In base R, this is similar to apply(matrix_object, 2, fun, simplify = FALSE).

Each of these function will loop on the matrixset object's matrices to apply the functions. In the case of apply_row() and apply_column(), an additional loop on the margin (row or column, as applicable) is executed, so that the functions are applied to each matrix and margin.

To see the functions in action, we will use the following object:

animals_ms

We will use the following custom printing functions for compactness purposes.

show_matrix <- function(x) {
  if (nrow(x) > 4) {
    newx <- head(x, 4)
    storage.mode(newx) <- "character"
    newx <- rbind(newx, rep("...", ncol(x)))
  }  else newx <- x
  newx
}
show_vector <- function(x) {
  newx <- if (length(x) > 4) {
    c(as.character(x[1:4]), "...")
  } else x
  newx
}
show_lst <- function(x) {
  lapply(x, function(u) {
    if (is.matrix(u)) show_matrix(u) else if (is.vector(u)) show_vector(u) else u
  })
}

So now, let's see the apply_matrix() in action.

library(magrittr)
library(purrr)
out <- animals_ms %>% 
   apply_matrix(exp,
                ~ mean(.m, trim=.1),
                foo=asinh,
                pow = ~ 2^.m,
                reg = ~ {
                  is_alive <- !is_extinct
                  lm(.m ~ is_alive + class)
                  })
# out[[1]] %>% map(~ if (is.matrix(.x)) {head(.x, 5)} else .x)
show_lst(out[[1]])

We have showcased several features of the apply_* functions:

• Many functions can be supplied at once.
• Functions can be supplied by bare function name. Note that this mean that only the current matrix will be used as input. You can also supply the function call or even, when submitting a one-sided formula, complex expressions.
• The name of the function result can be controlled.
• Object traits are accessible by bare name. The condition for this to work is that traits are unique across row and column annotation.

You probably have noticed the use of .m. This is a pronoun that is accessible inside apply_matrix() and refers to the current matrix in the internal loop. Similar pronouns exists for apply_row() and apply_column(), and they are respecticely .i and .j.

The returned object is a list of lists. The first layer is for each matrix and the second layer is for each function call.

Let's now showcase the row/column version with a apply_column() example:

out <- animals_ms %>% 
   apply_column(exp,
                ~ mean(.j, trim=.1),
                foo=asinh,
                pow = ~ 2^.j,
                reg = ~ {
                  is_alive <- !is_extinct
                  lm(.j ~ is_alive + class)
                  })
out[[1]] %>% map(show_lst)

The idea is similar, but in the returned object, there is a third list layer: the first layer for the matrices, the second layer for the columns (it would be rows for apply_row()) and the third layer for the functions.

Note as well the use of the .j pronoun instead of .m.

Grouped Data

The apply_* functions understand data grouping and will execute on the proper matrix/vector subsets.

animals_ms %>% 
  row_group_by(class) %>% 
  apply_matrix(exp,
               ~ mean(.m, trim=.1),
               foo=asinh,
               pow = ~ 2^.m,
               reg = ~ {
                 is_alive <- !is_extinct
                 lm(.m ~ is_alive)
                 })

As one can see, the output format differs in situation of grouping. We still end up with a list with an element for each matrix, but each of these element is now a tibble.

Each tibble has a column called .vals, where the function results are stored. This column is a list, one element per group. The group labels are given by the other columns of the tibble. For a given group, things are like the ungrouped version: further sub-lists for rows/columns - if applicable - and function values.

Simplified Results

Similar to the apply() function that has a simplify argument, the output structured can be simplified, baring two conditions:

• Each function returns a vector, where a vector is every object for which is.vector returns TRUE.
• Each vector must be of the same length $\geq$ 1.

If the conditions are met, each apply_* function has two simplified version available: _dfl and dfw.

Below is the _dfl flavor in action. We point out two things to notice:

• For apply_column_dfl (and _dfw), a .column column stores the column ID (.row for apply_row_*).
• We wrapped the lm result in a list so that the outcome is vector.

animals_ms %>% 
    apply_matrix_dfl(~ mean(.m, trim=.1),
                     MAD=mad,
                     reg = ~ {
                         is_alive <- !is_extinct
                         list(lm(.m ~ is_alive + class))
                     })

animals_ms %>% 
    apply_column_dfl(~ mean(.j, trim=.1),
                     MAD=mad,
                     reg = ~ {
                         is_alive <- !is_extinct
                         list(lm(.j ~ is_alive + class))
                     })

If using apply_column_dfw in this context, you wouldn't notice a difference in output format.

The difference between the two lies when the vectors are of length > 1.

animals_ms %>% 
    apply_row_dfl(rg = ~ range(.i),
                  qt = ~ quantile(.i, probs = c(.25, .75)))   

animals_ms %>% 
    apply_row_dfw(rg = ~ range(.i),
                  qt = ~ quantile(.i, probs = c(.25, .75)))   

We can observe three things:

1. dfl stands for long and stacks the elements of the function output into different rows, adding a column to identify the different elements.
2. dfw stands for wide and put the elements of the function output into different columns.
3. Element names are made unique if necessary.

Knowing the current context

It may happen that you need to get information about the current group. For this reason, the following context functions are made available:

• current_n_row() and current_n_column(). They each give the number of rows and columns, respectively, of the current matrix.

  They are the context equivalent of nrow() and ncol().

• current_row_info() and current_column_info(). They give access to the current row/column annotation data frame. The are the context equivlent of row_info() and column_info().

• row_pos() and column_pos(). They give the current row/column indices. The indices are the the ones before matrix subsetting.

• row_rel_pos() and column_rel_pos(). They give the row/column indices relative to the current matrix. They are equivalent to seq_len(current_n_row())/seq_len(current_n_column()).

For instance, a simple way of knowing the number of animals per group could be

animals_ms %>% 
    row_group_by(class) %>% 
    apply_matrix_dfl(n = ~ current_n_row()) %>% 
    .$msr

With common row and column annotation trait

The context functions can also be of use when one or more traits are shared (in name) between rows and columns.

Here's a pseudo-code example:

# ms_object %>% 
#     apply_matrix( ~ {
#       ctrt <- current_column_info()$common_trait
#       rtrt <- current_row_info()$common_trait
#       
#       do something with ctrt and rtrt
#     })

Pronouns, or dealing with ambiguous variables

It may happen that a variable in the calling environment shares its name with a trait of a matrixset object.

You can make it explicit which version of the variable you are using the pronouns .data (the trait annotation version) and .env.

Quasi quotation

reg_expr <- expr({
    is_alive <- !is_extinct
    list(lm(.j ~ is_alive + class))
})

animals_ms %>% 
    apply_column_dfl(~ mean(.j, trim=.1),
                     MAD=mad,
                     reg = ~ !!reg_expr)

Multivariate

mutate_matrix

matrixset documentation built on April 3, 2025, 6:32 p.m.