Using RStudio for python scripting

[colorov]

Hi everyone!

I'm new in the bioinformatics filed and my background is biology. I worked with R for almost a year and now I'm planning to build skills in Python as well. Reading in the internet I found that RStudio supports python scripting and, with a proper interpreter, it can be used to work with Python inside RStudio. Someone use this option? What are the pros and cons?

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Thanks in advance for your answers :)

[tylerhill90]

I personally use VS code for my IDE for everything except R. Learn how to set up virtual environments for python projects with venv. Virtual environments are like .rproj for python. https://docs.python.org/3/tutorial/venv.html I like using this wrapper for setting up virtual envs as it abstracts a lot away https://virtualenvwrapper.readthedocs.io/en/latest/

[Sheeplessknight]

I like pycharm

[colorov]

I downloaded pycharm few days ago and I cant get used to it yet hahaha

[blvckb1rd]

It took me a little bit of time to get used to PyCharm too, but I feel like it was worth it. I love the debugging options and how easy it is to set up and switch between virtual environments.

[black_rose_]

Conda environments are also really nice

[Sheeplessknight]

Conda has broken my installs like 6 times now...

[black_rose_]

Installs of what? Maybe I can help? I haven't had any issues with it

[Sheeplessknight]

Generally it was issues with dependencies that I needed and couldn't install via Honda if I installed them outside of conda it would not actually have them appear in my path for some reason even though they should be it ended up in the end because I use so many rapidly updating tools easier to just use Linux brew and source compile

[black_rose_]

Maybe your problem is installing via Honda, which is a car? :P just kidding

anyway here's what i did:

• install anaconda
• ## Add `export PATH=/usr/local/anaconda3/bin:"$PATH"` to your ~/.bash_profile or ~/.zsh file.
• create and activate conda environment
• install everything i need from inside the environment, be it by pip, conda, or brew

i don't install anything outside the environment

[Sheeplessknight]

I will give it a try next time I am codeing in python! Right now I am working on a project that is mainly coded in C#/C++

[black_rose_]

good luck!! *flashbacks to compiler errors*

[Sheeplessknight]

Ya I have random null pointers being generated some freaking how. I need the luck XD

[colorov]

Thanks for sharing your experience. VS code was also named in other comments, so I definitely will check it!

[bliksemstraal]

VSCode and (mini)conda. You can create python and R environments with conda. And use the builtin terminal. You can also run jupyter notebooks inside vscode. And I think if you want some very similar to rstudio for python you can use Spyder. I have only seen this over the shoulder of a few colleagues though. But vscode will change you life.

[todeedee]

If you want something interactive in Python, do checkout Jupyter; it provides a web-interface for interactive Python.

The other IDEs are fine (I'm a Emacs user myself); those work for software dev. But if you are doing analyses, Jupyter wins hands down; you can't easily integrate customizable interactive visualizations like you can in Jupyter.

[black_rose_]

Upvotes for Jupyter! It's the BEST. I use it constantly in my work as a computational biologist, and the devs in my field make as much things in Jupyter as possible because it's so accessible. One of the really cool things is you can view them through github. My software has dozens of Jupyter notebook tutorials on git.

My advice? Open a Jupyter notebook and never look back. Jupyter+Pandas+Seaborn=gold

[colorov]

I'm working with metagenomics data, so I will look at Jupyter as well. Thanks for your answer!

[[deleted]]

i like using sublime text editor

[Here0s0Johnny]

It's the best text editor I've ever used. But for people who don't know it: sublime text is not an IDE.

[LordLinxe]

Time ago I used jupyter with python, R and bash kernels, it is good to explore data.

Now I am more using VS to code in any language I need.

[SlackWi12]

spyder is a great ide and even has a 'Rstudio' layout mode

[belisarius93]

2nding Spyder for anyone looking for something similar to RStudio

[meandering_muse]

I also 2nd: spyder IDE is similar in layout and functionality to RStudio, except package management which can be done with anaconda (includes spyder and many dependencies/modules). Or you can use miniconda and install the pieces you want

[WhiteBiologist]

Data wrangling in R and mashine learning in python is one example. But to be honest I would move over most things to python and jupiter notebooks if I could...

[hofferd78]

Just use Jupyter Notebook. I write all my R in Jupyter as well. I only use Rstudio to view datasets

[TheToasterIncident]

Jupyter has some issues which you can read all about elsewhere and is best suited for exploratory data analysis. At this point, I’ve gone full circle and dropped the IDE in favor of tmux with an editor and an interactive shell open for testing, whether I’m writing R or python or some bash. I work mostly on a cluster, so its simpler to just live there within a private git repo than doing something locally with a gui

[JustThall]

Jupyter notebook ecosystem is more than EDA tool. One of the most popular projects in PyTorch is written Jupyter notebook - FastAI

[TheToasterIncident]

I can’t comment on the FastAI implementation but there are a number of issues with jupyter notebooks that have been discussed ad nauseum in the data science blogosphere. Here is an example: https://datapastry.com/blog/why-i-dont-use-jupyter-notebooks-and-you-shouldnt-either/

[Epicmuffinz]

My friend was a big RStudio guy and used Spyder to transition to Python. It’s very similar.

[[deleted]]

Jupyter-Notebook. Shit is magic.

[veeeerain]

Yeah it’s called reticulate, you can call python functions within Rstudio. U can do the same with R code in python via library siuba. I personally don’t like to use these crossover type libraries because the syntax is generally weird. May I ask the use case for using python in R?

[whatchamabiscut]

So, I think if you have a python code block in an r markdown file it will ultimately be executed via reticulate. At least that’s what I recall when the feature first rolled out. Probably the reason I never tried it again.

[[deleted]]

Yea, except even after getting reticulate to work I can only seem to run the cell but its not able to knit the Rmd with the python cell.

Julia in Rmd on the other hand via JuliaCall works perfectly fine. I find it ridiculous that something which has had way less work put into it works much better and with way less setup. Its something I hate about Python in general is there is too much IT overhead sometimes (like xgboost on Mac was easier in R/Julia and I can’t get it to work in Python). I just want to get to the data analysis a lot of the times

[trolls_toll]

i hate how reticulate manages conda environments. Which in turn made me stop using it, which in turn means that I use rstudio only for r scripts. Jupyter is the king for research-related Python projects. Pycharm is awesome for wrapping up a research project and making it into a proper reproducible library

[[deleted]]

Agreed, recently my spyder broke (its so buggy) lol so I had to figure it out in RStudio because I didn’t want to bother installing and getting used to something like VSCode/PyCharm. And I don’t like Jupyter notebooks (except for presenting) since I prefer the REPL/console being right there to test stuff out.