Clean up non-idiomatic code in vignette

from @antagomir

While I went through the vignette, I noticed some minor points that you may find useful for your next version. Use as you wish:

1. colData(cpd)$country (and other similar cases) can be also written more shortly just like: cpd$country
2. ggplot(as.data.frame(colData(cpd)))... -> the as.data.frame() was necessary until very recently, but not needed any more since the issue was [solved](https://github.com/tidyverse/ggplot2/issues/5390) ; the latest ggplot2 version allows this:
```
ggplot(colData(cpd))...
```
We are adding a reference to this data resource in the [OMA Gitbook](https://microbiome.github.io/OMA) (beta version, under active development)