tests/testthat/_snaps/data_classes.md

In calico/romic: R for High-Dimensional Omic Data

Test check_tidy_omic edge cases

Code
  check_tidy_omic(double_data_tidy, fast_check = FALSE)
Condition
  Error in `check_tidy_omic()`:
  ! 100 measurements were present multiple times with
       the same feature and sample primary keys

       For example:

       feature = 1 ; sample = 1
  feature = 1 ; sample = 2
  feature = 1 ; sample = 3
  feature = 1 ; sample = 4
  feature = 1 ; sample = 5
  feature = 1 ; sample = 6
  feature = 1 ; sample = 7
  feature = 1 ; sample = 8
  feature = 1 ; sample = 9
  feature = 1 ; sample = 10

Code
  create_tidy_omic(degenerate_attributes %>% select(-degen_sample_var),
  feature_pk = "features", sample_pk = "samples", feature_var = "degen_feature_var",
  verbose = FALSE)
Condition
  Error in `check_tidy_omic()`:
  ! "degen_feature_var" was duplicated for 10 features
  this variable should not be a feature attribute.

Code
  create_tidy_omic(degenerate_attributes %>% select(-degen_feature_var),
  feature_pk = "features", sample_pk = "samples", sample_var = "degen_sample_var",
  verbose = FALSE)
Condition
  Error in `check_tidy_omic()`:
  ! "degen_sample_var" was duplicated for 10 features
  this variable should not be a feature attribute.

Factor primary keys are preserved when converting from a tidy to a triple

Code
  create_tidy_omic(three_col_df_fct, feature_pk = "features", sample_pk = "samples",
    sample_vars = "measurement", feature_vars = "measurement", verbose = FALSE)
Condition
  Error in `create_tidy_omic()`:
  ! measurement were assigned to multiple classes of variables each variable should only belong to one class

Catch corner cases when reading wide data

Code
  convert_wide_to_tidy_omic(wide_df_nonunique_feature_id, feature_pk = "name")
Condition
  Warning in `convert_wide_to_tidy_omic()`:
  4 rows did not contain a unique name; adding extra variables 'unique_name' & 'entry_number' to distinguish them
  Warning:
  `mutate_()` was deprecated in dplyr 0.7.0.
  i Please use `mutate()` instead.
  i See vignette('programming') for more help
Message
  1 measurement variables were defined as the
  left overs from the specified feature and sample varaibles:
  abundance
Output
  $data
  # A tibble: 19,500 x 5
     name    entry_number unique_name sample abundance                            
     <chr>          <int> <chr>       <chr>  <chr>                                
   1 YOL029C            1 YOL029C-1   BP     biological process unknown           
   2 YOL029C            2 YOL029C-2   BP     cytokinesis, completion of separation
   3 YOL029C            3 YOL029C-3   BP     biological process unknown           
   4 YOL029C            4 YOL029C-4   BP     cell wall organization and biogenesis
   5 YOL029C            5 YOL029C-5   BP     cell wall organization and biogenesi~
   6 FKH1               1 FKH1        BP     pseudohyphal growth*                 
   7 HOC1               1 HOC1        BP     cell wall mannoprotein biosynthesis* 
   8 CSN12              1 CSN12       BP     adaptation to pheromone during conju~
   9 YAL046C            1 YAL046C     BP     biological process unknown           
  10 SLG1               1 SLG1        BP     cell wall organization and biogenesi~
  # i 19,490 more rows

  $design
  $design$features
  # A tibble: 3 x 2
    variable     type               
    <chr>        <chr>              
  1 unique_name  feature_primary_key
  2 name         character          
  3 entry_number integer

  $design$samples
  # A tibble: 1 x 2
    variable type              
    <chr>    <chr>             
  1 sample   sample_primary_key

  $design$measurements
  # A tibble: 3 x 2
    variable    type               
    <chr>       <chr>              
  1 unique_name feature_primary_key
  2 sample      sample_primary_key 
  3 abundance   character

  $design$feature_pk
  [1] "unique_name"

  $design$sample_pk
  [1] "sample"


  attr(,"class")
  [1] "tidy_omic" "tomic"     "general"

Find primary or foreign keys in tomic table

Code
  get_identifying_keys(brauer_2008_triple, "foo")
Condition
  Error in `get_identifying_keys()`:
  ! Assertion on 'table' failed: Must be element of set {'features','samples','measurements'}, but is 'foo'.

Test that get_tomic_table() can retrieve various tables

Code
  infer_tomic_table_type(simple_tidy, samples_df %>% rename(fake_samples = samples))
Condition
  Error in `infer_tomic_table_type()`:
  ! based on the "tomic" primary keys, tomic_table doesn't appear to
         be features, samples or measurements

Catch corner cases when interconverting tomics

Code
  check_tomic(mtcars)
Condition
  Error in `check_tomic()`:
  ! Assertion on 'tomic' failed: Must inherit from class 'tomic', but has class 'data.frame'.

Code
  tomic_to(romic::brauer_2008_tidy, "foo")
Condition
  Error in `tomic_to()`:
  ! Assertion on 'to_class' failed: Must be element of set {'tidy_omic','triple_omic'}, but is 'foo'.

calico/romic documentation built on Sept. 27, 2024, 7:16 p.m.