ggplot2 VS Biopython

ggplot2

I got the list of five-letter words from the words package in R, created the QWERTY keyboard grid with base R and tibble, and visualized the data with geom_tile in the ggplot2 package.

Thanks, it's an interesting idea! I definitely could implement this with scale_fill_gradientn) in ggplot2.

I used the ggplot2 package in R to create these figures.

This might not be at the top of your list, but science fiction often presents advanced data analysis and visualization technologies. Open source data analysis tools such as Python's Pandas and R's ggplot2 have revolutionized the field, making complex data manipulation and visualization accessible to all. In the science fiction novel The Martian, astronaut Mark Watney uses a variety of data analysis and visualization tools to survive on Mars. He uses Python's Pandas to clean and organize data, and he uses R's ggplot2 to create visualizations of his data. These tools allow him to make sense of the vast amounts of data and help him to make critical decisions about his survival.

Sorry about the slow reply, but the auto-moderator seems to be deleting my comments (for some unknown reason). I will try once more: the geom_tile function in ggplot2.

Visual cues are a much better idea, thanks! Unfortunately, I don't know how to do that in ggplot2, either (I created these figures in R).

Usearch will do all-against-all comparisons, cluster sequences, and produce alignments for each cluster. You can set the clustering threshold (proportion of residues identical). The alignments are in fasta format, which is pretty standard. If all you want is basic similarity it might be easiest to just write something that calculates normalized Hamming distances (typically called p-distances in the molecular evolution literature) between pairs of sequences. I suspect the biopython fasta reader (you can install biopython from https://biopython.org/) will be good enough.

Yes, the computing tool for biological computation.

Beside that their core lectures to non-computer scientists are public (survey), workshops by software carpentry move around the globe. Maybe your intent to seed hands-on knowledge is in similar tune before heading for biopython, bioperl, bioawk. It doesn't hurt to tap into resources initially written for non-labrats either, e.g. about regular expressions by programming historian.

Well, what language do you want to learn? What is your background so far? Assuming it is more on the side of biology, software carpentry's Python may eventually lead to biopython? Though there equally is a chance for AWK (Hack the planet's text! and bioawk...

I think you mind find something of a community around BioPython, which might be helpful. Just looking at the capabilities will probably be instructive as well.

Python is the main programming language I use nowadays. In particular numpy and pandas are of course extremely useful. I also use biopython package - a collection of software tools for biological computation written in Python by an international group of researchers and developers.