umr1283 / carot

Centralised and Automated RepOrting Tools

UMR 1283 - Project Template

You can install umr1283 with:

remotes::install_github("umr1283/umr1283")

The default project directory architecture from umr1283::create_project (compatible with RStudio Project Wizard) is as follow:

library(umr1283)
create_project(path = "my-project", analyst_name = "UMR1283")

tree -a my-project
#> my-project/
#> ├── data
#> ├── .devcontainer
#> │   ├── devcontainer.json
#> │   └── Dockerfile
#> ├── docs
#> ├── .gitignore
#> ├── logs
#> ├── my-project.Rproj
#> ├── outputs
#> ├── README.md
#> ├── renv
#> ├── reports
#> ├── .Rprofile
#> ├── scripts
#> │   ├── 00-targets.R
#> │   ├── _dependencies.R
#> │   └── tar-utils
#> ├── _targets
#> └── _targets.R
#> 
#> 10 directories, 9 files

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Getting help

If you encounter a clear bug, please file a minimal reproducible example on GitHub.
For questions and other discussion, please open a discussion on GitHub.

carot's Issues

Condition length when checking input files `estimate_ethnicity`

In estimate_ethnicity, test isnot robust due to condition length exceeding one.

list_input <- check_input(input = input_vcfs)
Warning messages:
1: In if (!fs::is_dir(input) & !fs::is_file(input)) { :
  the condition has length > 1 and only the first element will be used
2: In if (fs::is_dir(input)) { :
  the condition has length > 1 and only the first element will be used

`pca_report` do not use the parameter `id_var`

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The function pca_report has the id_var parameter that let us think we can choose the name if the column id, but the default value "Sample_ID" is used to create the column in the dataset pca_dfxy. So the final left_join has an error if we do not use the default setting id_var = "Sample_ID "

library(tidyverse)
CARoT::pca_report(
    data = mtcars, 
    design = tibble(
        My_Sample_ID = row.names(mtcars), 
        First_Letter = substring(My_Sample_ID, 1, 1)
    ), 
    id_var = "My_Sample_ID",
    technical_vars = c("First_Letter"), 
    n_comp = 2, 
    fig_n_comp = 3,
    title_level = 3
)
#> [CARoT] Quality-Control started ...
#> `by` can't contain join column `My_Sample_ID` which is missing from RHS

After inspecting the script, it seems that the error come from this part :

pca_dfxy <- dplyr::mutate(.data = pca_dfxy, Sample_ID = as.character(colnames(data)))
pca_dfxy <- as.data.frame(dplyr::left_join(x = design, y = pca_dfxy, by = id_var))