plot_differential_outcomes: Arguments imply differing number of rows

[HDash]

New error on check(), appearing after all the January merges. I can confirm this error was not present when I was working on my branch back in December.

One of the test cases for plot_differential_outcomes fails.

Reprex

Code taken from test_plot_differential_outcomes-

devtools::load_all()
#> ℹ Loading MSTExplorer

results <- load_example_results()
results <- add_symptom_results(results = results,
                                 celltype_col="cl_name",
                                 proportion_driver_genes_symptom_threshold=.25)
#> Adding symptom-level results.
#> Reading cached RDS file: phenotype_to_genes.txt
#> + Version: v2024-02-08
#> Subsetting results by q_threshold and effect.
#> 46,514 associations remain after filtering.
#> Mapping cell types to cell ontology terms.
#> Adding stage information.
#> Adding genes and disease IDs.
#> Reading cached RDS file: phenotype_to_genes.txt
#> + Version: v2024-02-08
#> Loading ctd_DescartesHuman.rds
#> Loading ctd_HumanCellLandscape.rds
results <- HPOExplorer::add_gpt_annotations(results)
#> Translating ontology terms to ids.
#> Reading cached RDS file: phenotype_to_genes.txt
#> + Version: v2024-12-12
#> 151 phenotypes do not have matching HPO IDs.
#> Reading in GPT annotations for 16,982 phenotypes.
annot <- HPOExplorer::load_phenotype_to_genes(3)
#> Reading cached RDS file: phenotype.hpoa
#> + Version: v2024-02-08
diseases_with_hypotonia <- annot[hpo_id=="HP:0001319"]$disease_id |>unique()## Neonatal hypotonia
phenotypes_with_hypotonia <- annot[disease_id %in% diseases_with_hypotonia]$hpo_id |> unique()
results[,group:="Hypotonia"]
p1b <- plot_differential_outcomes(results,
                                    max_facets=10,
                                   facet_var = "disease_name",
                                   y_var = "blindness",
                                   run_stats = TRUE)
#> Adding disease_name and disease_description.
#> Loading required namespace: paletteer
#> Loading required namespace: ggstatsplot
#> Valid facets: 8210
#> Error in data.frame(..., check.names = FALSE): arguments imply differing number of rows: 0, 1

^{Created on 2025-01-09 with reprex v2.1.1}

Using the latest version of HPOExplorer@master and KGExplorer@master.

Session Info

devtools::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.4.2 (2024-10-31)
#>  os       macOS Sequoia 15.2
#>  system   aarch64, darwin20
#>  ui       X11
#>  language (EN)
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
#>  tz       Europe/London
#>  date     2025-01-08
#>  pandoc   3.5 @ /opt/homebrew/bin/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package     * version  date (UTC) lib source
#>  cachem        1.1.0    2024-05-16 [1] CRAN (R 4.4.0)
#>  cli           3.6.3    2024-06-21 [1] CRAN (R 4.4.0)
#>  devtools      2.4.5    2022-10-11 [1] CRAN (R 4.4.0)
#>  digest        0.6.37   2024-08-19 [1] CRAN (R 4.4.1)
#>  ellipsis      0.3.2    2021-04-29 [1] CRAN (R 4.4.0)
#>  evaluate      1.0.1    2024-10-10 [1] CRAN (R 4.4.1)
#>  fastmap       1.2.0    2024-05-15 [1] CRAN (R 4.4.0)
#>  fs            1.6.5    2024-10-30 [1] CRAN (R 4.4.1)
#>  glue          1.8.0    2024-09-30 [1] CRAN (R 4.4.1)
#>  htmltools     0.5.8.1  2024-04-04 [1] CRAN (R 4.4.0)
#>  htmlwidgets   1.6.4    2023-12-06 [1] CRAN (R 4.4.0)
#>  httpuv        1.6.15   2024-03-26 [1] CRAN (R 4.4.0)
#>  knitr         1.49     2024-11-08 [1] CRAN (R 4.4.1)
#>  later         1.4.1    2024-11-27 [1] CRAN (R 4.4.1)
#>  lifecycle     1.0.4    2023-11-07 [1] CRAN (R 4.4.0)
#>  magrittr      2.0.3    2022-03-30 [1] CRAN (R 4.4.0)
#>  memoise       2.0.1    2021-11-26 [1] CRAN (R 4.4.0)
#>  mime          0.12     2021-09-28 [1] CRAN (R 4.4.0)
#>  miniUI        0.1.1.1  2018-05-18 [1] CRAN (R 4.4.1)
#>  pkgbuild      1.4.5    2024-10-28 [1] CRAN (R 4.4.1)
#>  pkgload       1.4.0    2024-06-28 [1] CRAN (R 4.4.0)
#>  profvis       0.4.0    2024-09-20 [1] CRAN (R 4.4.1)
#>  promises      1.3.2    2024-11-28 [1] CRAN (R 4.4.1)
#>  purrr         1.0.2    2023-08-10 [1] CRAN (R 4.4.0)
#>  R6            2.5.1    2021-08-19 [1] CRAN (R 4.4.0)
#>  Rcpp          1.0.13-1 2024-11-02 [1] CRAN (R 4.4.1)
#>  remotes       2.5.0    2024-03-17 [1] CRAN (R 4.4.0)
#>  reprex        2.1.1    2024-07-06 [1] CRAN (R 4.4.0)
#>  rlang         1.1.4    2024-06-04 [1] CRAN (R 4.4.0)
#>  rmarkdown     2.29     2024-11-04 [1] CRAN (R 4.4.1)
#>  rstudioapi    0.17.1   2024-10-22 [1] CRAN (R 4.4.1)
#>  sessioninfo   1.2.2    2021-12-06 [1] CRAN (R 4.4.0)
#>  shiny         1.10.0   2024-12-14 [1] CRAN (R 4.4.1)
#>  urlchecker    1.0.1    2021-11-30 [1] CRAN (R 4.4.0)
#>  usethis       3.1.0    2024-11-26 [1] CRAN (R 4.4.1)
#>  vctrs         0.6.5    2023-12-01 [1] CRAN (R 4.4.0)
#>  withr         3.0.2    2024-10-28 [1] CRAN (R 4.4.1)
#>  xfun          0.50     2025-01-07 [1] CRAN (R 4.4.1)
#>  xtable        1.8-4    2019-04-21 [1] CRAN (R 4.4.0)
#>  yaml          2.3.10   2024-07-26 [1] CRAN (R 4.4.0)
#> 
#>  [1] /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────

^{Created on 2025-01-08 with reprex v2.1.1}

[HDash]

R CMD Check output

── Error ('test-plot_differential_outcomes.R:39:3'): plot_differential_outcomes works ──
Error in `data.frame(..., check.names = FALSE)`: arguments imply differing number of rows: 0, 1
Backtrace:
    ▆
 1. └─MSTExplorer::plot_differential_outcomes(...) at test-plot_differential_outcomes.R:39:3
 2.   └─MSTExplorer:::plot_differential_outcomes_ggstatsplot(...)
 3.     └─base::lapply(...)
 4.       └─MSTExplorer (local) FUN(X[[i]], ...)
 5.         └─base::tryCatch(...)
 6.           └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 7.             └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 8.               └─value[[3L]](cond)

[ FAIL 2 | WARN 1873 | SKIP 0 | PASS 60 ]