tests/testthat/_snaps/mutates.md

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

center_tomic centers selected variables in a tomic

Code
  center_tomic(brauer_2008_tidy, measurement_vars = "foo")
Condition
  Error in `center_tomic()`:
  ! foo are not valid numeric or integer measurement variables.
          Valid measurements are: expression

Sort tables and update primary keys with new sort

Code
  .
Output
  # A tibble: 36 x 4
     sample nutrient    DR order
     <chr>  <chr>    <dbl> <int>
   1 P0.05  P         0.05     1
   2 P0.1   P         0.1      2
   3 P0.15  P         0.15     3
   4 P0.2   P         0.2      4
   5 P0.25  P         0.25     5
   6 P0.3   P         0.3      6
   7 G0.25  G         0.25     7
   8 G0.3   G         0.3      8
   9 U0.25  U         0.25     9
  10 U0.3   U         0.3     10
  # i 26 more rows

Code
  .
Condition
  Error in `sort_triple_hclust()`:
  ! bar is not present in measurements, valid value_vars include:
  expression

Factor levels can be updated using a list of factor orders

Code
  brauer_w_mystery_nutrients <- update_sample_factors(brauer_2008_tidy_w_NAs,
    list(nutrient = NUTRIENT_ORDER))
Message
  ! NA was present in the sample metadata's nutrient field but did not have a corresponding factor level in the `factor_levels` list. They will be added to the end of the specified factor levels
  ! The nutrient field in the sample metadata contains 2 NA values. These entries will be replaced with an "unspecified" level.

Code
  reordered_tidy <- update_sample_factors(brauer_2008_tidy, list(nutrient = CONFUSED_NUTRIENT_ORDER))
Message
  ! "G" was present in the sample metadata's nutrient field but did not have a corresponding factor level in the `factor_levels` list. They will be added to the end of the specified factor levels
  ! "C" was present in `factor_levels` for nutrient but did not have a corresponding entry in the sample metadata.

Code
  update_sample_factors(brauer_2008_tidy, list(nutrient = 1:5))
Condition
  Error in `set_factor_levels()`:
  ! The factor levels for nutrient were "integer". This should be a character vector.

Code
  update_sample_factors(brauer_2008_tidy, list(nutrient = c("G", "G", "N", "L")))
Condition
  Error in `set_factor_levels()`:
  ! 1 factor levels was duplicated in the `factor_levels` specification for "nutrient": G

Code
  update_sample_factors(brauer_2008_tidy, list(DR = seq(0.05, 0.3, by = 0.05)))
Condition
  Error in `set_factor_levels()`:
  ! The factor levels for DR were "numeric". This should be a character vector.

Update tidy omics with new added variables

Code
  update_tidy_omic(tidy_omic, updated_tidy_data, c())
Condition
  Error in `update_tidy_omic()`:
  ! updated_tidy_data contains 1
  - new fields: new_sample_var.
  - Add these to "new_variable_tables" so that romic know how to
  - use them.

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