How to annotate a matrixset

Annotate at object creation

We will use the same example as in the introduction vignette, the Animals object.

library(tidyverse)
#> Warning: package 'ggplot2' was built under R version 4.3.1
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)

Annotations are internally stored as [tibble::tibble()] objects and can be viewed as simple data bases. As such, a key is needed to uniquely identify the rows or the columns. This key is the rownames for row annotation and colnames for column annotation.

This key is called the tag and, unless specified otherwise at the matrixset creation, is stored as .rowname/.colname. This special tag can almost be used as any other annotation traits - see Applying Functions.

When using an external data.frame to create new annotations, the data frame must contain this key - it doesn’t have to be called .rowname/.colname - in a single column.

Moreover, the key values must correspond to rownames/colnames. Values that do not match will simply left out.

To use the annotation at creation, simply use a command like this

ms <- matrixset(msr = animals, log_msr = log_animals, row_info = animal_info,
                row_key = "Animal")
ms
#> matrixset of 2 28 × 2 matrices
#> 
#> matrix_set: msr 
#> A 28 × 2 <dbl> matrix
#>                   body  brain
#> Mountain beaver   1.35   8.10
#>             ...    ...    ...
#>             Pig 192.00 180.00
#> 
#> matrix_set: log_msr 
#> A 28 × 2 <dbl> matrix
#>                 body brain
#> Mountain beaver 0.30  2.09
#>             ...  ...   ...
#>             Pig 5.26  5.19
#> 
#> 
#> row_info:
#> # A tibble: 28 × 3
#>    .rowname        is_extinct class       
#>    <chr>           <lgl>      <chr>       
#>  1 Mountain beaver FALSE      Rodent      
#>  2 Cow             FALSE      Ruminant    
#>  3 Grey wolf       FALSE      Canine      
#>  4 Goat            FALSE      Ruminant    
#>  5 Guinea pig      FALSE      Rodent      
#>  6 Dipliodocus     TRUE       Dinosaurs   
#>  7 Asian elephant  FALSE      Elephantidae
#>  8 Donkey          FALSE      Equidae     
#>  9 Horse           FALSE      Equidae     
#> 10 Potar monkey    FALSE      Primate     
#> # ℹ 18 more rows
#> 
#> 
#> column_info:
#> # A tibble: 2 × 1
#>   .colname
#>   <chr>   
#> 1 body    
#> 2 brain

Notice how we used the row_key argument to specify how to link the two objects together.

Replacing an annotation tibble

The internal tibble can be replaced by a new one. This could be an interesting possibility to add annotations to an existing matrixset object where none were registered.

To do so, you can simply do

row_info(ms) <- animal_info %>% rename(.rowname = Animal)

For the operation to work, a column called .rowname (or more generally, what is returned by row_tag()) must be part of the data frame.

The column equivalents are column_info and column_tag.

Annotation tibble replacement works even if annotations were registered. Be aware of two things:

Old annotations will be lost, unless an exact copy is also in the new data frame
In the case of grouping, the grouping structure will potentially change. When possible, it will be kept/updated, but it will be otherwise removed.

Appending data frame values to the annotation tibble

This is equivalent to performing a mutating join (default: [dplyr::left_join()], though all mutating joins - except cross-joins - are available via the type argument) between the matrixset (.ms) object’s annotation tibble and a data.frame (.y).

The by argument will determine how to join the two data.frames together, so it is not necessary for y to have a .rowname/.colname column. But when the by argument is not provided, a natural join is performed.

One behavior that differs with a true mutating join, is that when a row from .ms matches more than one row in .y, no row duplication will be performed. Instead, a condition error will be issued. This is to preserve the matrixset property that all row names (and column names) must be unique.

matrixset(msr = animals, log_msr = log_animals) %>% 
    join_row_info(animal_info, by = c(".rowname" = "Animal"))

The data frame can be taken from a second matrixset object

Indeed! In using join_row_info()/join_column_info(), .y can be a matrixset object, in which case the appropriate annotation tibble will be used.

The only difference is when using the default by = NULL argument. In that case the row/column tag of each object is used.

Creating new annotations from existing ones (and modify/delete)

If you are familiar with dplyr::mutate(), then you know almost everything you need to know about using annotate_row() and annotate_column().

ms <- matrixset(msr = animals, log_msr = log_animals) %>% 
    join_row_info(animal_info, by = c(".rowname" = "Animal")) %>% 
    annotate_column(unit = case_when(.colname == "body" ~ "kg",
                                     TRUE ~ "g")) %>% 
    annotate_column(us_unit = case_when(unit == "kg" ~ "lb",
                                        TRUE ~ "oz"))
column_info(ms)
#> # A tibble: 2 × 3
#>   .colname unit  us_unit
#>   <chr>    <chr> <chr>  
#> 1 body     kg    lb     
#> 2 brain    g     oz

You can decide that you don’t need two unit systems and keep only one

ms <- ms %>% annotate_column(us_unit = NULL)
column_info(ms)
#> # A tibble: 2 × 2
#>   .colname unit 
#>   <chr>    <chr>
#> 1 body     kg   
#> 2 brain    g

Creating new annotations from applying function(s) to an object’s matrix

Applying functions to a matrixset’s matrices is covered in the Applying Functions vignette.

The idea here is the same, but with the added benefit that the function result is stored directly as annotation for the matrixset object.

ms %>% 
    annotate_row_from_apply(msr, ratio_brain_body = ~ .i[2]/(10*.i[1])) %>% 
    row_info()
#> # A tibble: 28 × 4
#>    .rowname        is_extinct class        ratio_brain_body
#>    <chr>           <lgl>      <chr>                   <dbl>
#>  1 Mountain beaver FALSE      Rodent               0.6     
#>  2 Cow             FALSE      Ruminant             0.0910  
#>  3 Grey wolf       FALSE      Canine               0.329   
#>  4 Goat            FALSE      Ruminant             0.416   
#>  5 Guinea pig      FALSE      Rodent               0.529   
#>  6 Dipliodocus     TRUE       Dinosaurs            0.000427
#>  7 Asian elephant  FALSE      Elephantidae         0.181   
#>  8 Donkey          FALSE      Equidae              0.224   
#>  9 Horse           FALSE      Equidae              0.126   
#> 10 Potar monkey    FALSE      Primate              1.15    
#> # ℹ 18 more rows

When groups are registered, results are spread using tidyr::pivot_wider().

ms %>% 
    row_group_by(class) %>% 
    annotate_column_from_apply(msr, mean) %>% 
    column_info()
#> # A tibble: 2 × 13
#>   .colname unit  Canine Dinosaurs Elephantidae Equidae Feline Macropodidae
#>   <chr>    <chr>  <dbl>     <dbl>        <dbl>   <dbl>  <dbl>        <dbl>
#> 1 body     kg      36.3   36033.         4600.    354.   51.6           35
#> 2 brain    g      120.       91.5        5158.    537    91.3           56
#> # ℹ 5 more variables: Primate <dbl>, Rodent <dbl>, Ruminant <dbl>, Sus <dbl>,
#> #   Talpidae <dbl>