cpvt-serca_paper

This is the accompanying GitHub repository containing most of the analyis from the publication Uptake-leak balance of SR Ca²⁺ determines arrhythmogenic potential of RyR2R420Q^+/− cardiomyocytes DOI:10.1016/j.yjmcc.2022.05.011 by Ruben Lopez, Ernst Niggli, Radoslav Yanicek, Miguel Fernandez-Tenorio, Ana Gomez and others.

The raw data from this paper can be accessible in the Zenodo repository

Compile

The following instructions describe how to reproduce a copy of the source files for most of our analysis of Ca²⁺ waves in our manuscript. this isntructions are heavily inspired by Aaron Peikert and you can read more here. We describe reproducible workflows, and create .html documents as well as individual figures, summary statistics and test performed in our data. Either, you can go the ‘standard’ way of downloading a local copy of the repository and knit each markdown file(s) located under the folder code using RStudio, or you can use the reproducible workflow as suggested and use Make to create a container and build the final results in exactly the same virtual computational environment that we used to render the .html

Standard Way

Requires: Git, RStudio, pandoc, pandoc-citeproc, rmarkdown & renv.

Open RStudio -> File -> New Project -> Version Control -> Git

Insert:

https://github.com/rjlopez2/CPVT-SERCA_paper

you have to check if this actually work with the {renv} package

to restore all the dependencies, run from within the RStudio’s console this command and follow the instructions:

renv::restore()

Go to the folder code and open full_analysis.Rmd click on Knit.

Do the same for the additional markdown files.

Using a Reproducible Workflow

Does not require R or RStudio, but make & docker.

Before you start, make sure that you have installed in your machine make and docker. In this tutorial is fairly well explained how to install it depending on your system.

Execute in Terminal:

git clone https://github.com/rjlopez2/cpvt-serca_paper.git
cd cpvt-serca_paper
make build
make all DOCKER=TRUE OUTPUT=TRUE

if you wish not to have the output (summary tables and figures), but just the html files, run the last line with OUTPUT=FALSE

Note: Windows user need to manually edit the Makefile and set current_path to the current directory and use make all DOCKER=TRUE WINDOWS=TRUE. We hope that future releases of Docker for Windows will not require that workaround.

Rebuild Everything

In case you experience some unexpected behavior with this workflow, you should check that you have the most recent version (git pull), rebuild the docker image (make build) and force the rebuild of all targets (make -B DOCKER).

git pull && make rebuild && make -B DOCKER=TRUE

Session Info

sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.2.0 (2022-04-22)
#>  os       Ubuntu 20.04.4 LTS
#>  system   x86_64, linux-gnu
#>  ui       RStudio
#>  language (EN)
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
#>  tz       Etc/UTC
#>  date     2022-09-08
#>  rstudio  2022.02.3+492 Prairie Trillium (server)
#>  pandoc   2.17.1.1 @ /usr/lib/rstudio-server/bin/quarto/bin/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────
#>  package     * version date (UTC) lib source
#>  cli           3.3.0   2022-04-25 [1] RSPM (R 4.2.0)
#>  digest        0.6.29  2021-12-01 [1] RSPM (R 4.2.0)
#>  evaluate      0.15    2022-02-18 [1] RSPM (R 4.2.0)
#>  fastmap       1.1.0   2021-01-25 [1] RSPM (R 4.2.0)
#>  htmltools     0.5.3   2022-07-18 [1] CRAN (R 4.2.0)
#>  knitr         1.39    2022-04-26 [1] RSPM (R 4.2.0)
#>  magrittr      2.0.3   2022-03-30 [1] RSPM (R 4.2.0)
#>  rlang         1.0.4   2022-07-12 [1] CRAN (R 4.2.0)
#>  rmarkdown     2.16    2022-08-24 [1] CRAN (R 4.2.0)
#>  rstudioapi    0.13    2020-11-12 [1] RSPM (R 4.2.0)
#>  sessioninfo   1.2.2   2021-12-06 [1] RSPM (R 4.2.0)
#>  stringi       1.7.6   2021-11-29 [1] RSPM (R 4.2.0)
#>  stringr       1.4.0   2019-02-10 [1] RSPM (R 4.2.0)
#>  xfun          0.31    2022-05-10 [1] RSPM (R 4.2.0)
#>  yaml          2.3.5   2022-02-21 [1] RSPM (R 4.2.0)
#> 
#>  [1] /usr/local/lib/R/site-library
#>  [2] /usr/local/lib/R/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
# 
# Sys.getenv("R_HOME")
# readLines("/System/Library/CoreServices/SystemVersion.plist")
# utils:::.osVersion()
# 
# debug(utils:::.osVersion)
# utils:::.osVersion()