> For the complete documentation index, see [llms.txt](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://laboratory-of-lipid-metabolism-a.gitbook.io/omics-data-visualization-in-r-and-python/metabolites-and-lipids-descriptive-statistical-analysis-in-r/basic-plotting-in-r.md).

# Basic plotting in R

R is an excellent solution for producing graphics depicting descriptive statistics. Among the R packages, there are various solutions suitable for beginners, e.g., dlookr, DataExplorer, ggpubr, or ggstatsplot, which create charts via uncomplicated functions. More experienced users select libraries that offer a high level of flexibility, like ggplot2 or plotly. However, in some cases, the code can become too complex for a beginner. 

Here, we will show you how to prepare essential charts in R, which are frequently used in lipidomics and metabolomics studies. We will start every subchapter with the simplest method, progressing toward ggplot2 or plotly solution. We will begin with setting the working directory (wd) and the installation of all necessary packages:

```r
# Set your working directory through setwd("dir").
# If your files with data are on the D drive, in the "Data analysis folder," then use:
setwd("D:/Data analysis")

# Installing packages for the data visualization:
# 1. ggpubr
install.packages("ggpubr")

# 2. ggstatsplot
install.packages("ggstatsplot")

# 3. dlookr -- already installed if you follow the handbook
install.packages("devtools")
devtools::install_github("choonghyunryu/dlookr")

# 4. DataExplorer -- already installed if you follow the handbook
install.packages("DataExplorer")

# 5. plotly
install.packages("plotly")

# 6. ggplot2 -- it is a part of the tidyverse collection!
install.packages("ggplot2")
```

Here, we keep using the lipidomics data set we shared at the beginning of the Gitbook. Now, we are ready to prepare the first plots in R.


---

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