index.qmd

# Preface {.unnumbered}

This is the R Seahorse data analysis manual using functions from the Seahtrue package.
Its purpose is to demonstrate and educate how to use R for Extracellular Flux analysis.
We use a dedicated data analysis pipeline for quality control and advanced plotting of the data.

You can run R this manual in your browser and do not need to install any R or Rstudio software on your computer.

::: callout-note
The manual is targeted to all levels of learning, meaning that also interested learners without any R background or programming knowledge can use it
:::

::: callout-tip
To turn your `.asyr` Seahorse Wave file into an excel `.xlsx` file, you can use the Seahorse Wave desktop software or the Seahorse analytics website from Agilent:

<https://seahorseanalytics.agilent.com>

Lots of info regarding Seahorse analysis including how it works and how to run experiments is available from the Agilent website

All things lab - How to run an assay:

<https://www.agilent.com/en/product/cell-analysis/how-to-run-an-assay>

All other Agilent Seahorse info:

<https://www.agilent.com/en/products/cell-analysis/how-seahorse-xf-analyzers-work>
:::

## Resources

### Free books

[Telling Stories with data]{.underline}

*Excellent very complete overview covering basic R coding, communicating science, and statistics*. These two chapters are particularly good:

-   Clean and prepare <https://tellingstorieswithdata.com/09-clean_and_prepare.html>

-   appendix 1: R essentials <https://tellingstorieswithdata.com/20-r_essentials.html>

[R for data Science]{.underline}

*The go-to book when you want to get familiar with R and tidy from Hadley Wickham and others from Posit* <https://r4ds.hadley.nz/>

Nice sections, for example:

-   ggplot basics <https://r4ds.hadley.nz/data-visualize>

-   lubridate date and time basics <https://r4ds.hadley.nz/datetimes>

[Functional programming book]{.underline}

*Nice visualizations of data structures and operations*

-   vectors, lists, tibbles <https://dcl-prog.stanford.edu/data-structure-basics.html>

-   map and purrr <https://dcl-prog.stanford.edu/purrr-basics.html>

[Fundamentals of Data Visualization](https://clauswilke.com/dataviz/)

*Everything you want to know about visualizing data using ggplot, with beautifull plots. Also, all code fully available on github*

-   associations (scatter plots etc) <https://clauswilke.com/dataviz/visualizing-associations.html>

-   uncertainty (error bars and distirbutions etc) <https://clauswilke.com/dataviz/visualizing-uncertainty.html>

-   ggplot tutorial by Cedric Scherer
<https://www.cedricscherer.com/2019/08/05/a-ggplot2-tutorial-for-beautiful-plotting-in-r/>

### Webr/WASM

webr REPL - a full complete rstudio-like R environment in the browser <https://webr.r-wasm.org/latest/>

Webr/wasm presentation bob rudis - (how I got interested in webr/wasm) - <https://www.youtube.com/watch?v=inpwcTUmBDY>

Webr manual <https://docs.r-wasm.org/webr/latest/>

Webr on github <https://github.com/r-wasm/webr/>

### Other info

Learn to purrr, Rebecca Barter - <https://www.rebeccabarter.com/blog/2019-08-19_purrr>

### Movies:

Purrr and map functions explained by Hadley - <https://www.youtube.com/watch?v=EGAs7zuRutY>


## R fun

<https://twitter.com/rafamoral/status/1571622591219236864?s=20&t=RJWOSe30-8bbDxgLIamRUQ>