Plotting in R for Biologists -- Lesson 1: From data to plot with a few magic words

Lesson 1: Hit the ground running — From data to plot with a few magic words

UPDATE:
* In a new version of R, you may need to add `stringsAsFactors = TRUE` when importing data from a CSV file.

You can put in $0 to get the course for free, I really don't mind, and then you can watch it all without distractions and ads for better learning :)

Analyze your data yourself, beyond the limitations of Excel and without waiting for a collaborator.

My name is Maria Nattestad and I'm a computational biologist at Cold Spring Harbor Laboratory. Whenever I talk to other grad students and post-docs about their experience with analyzing their data, the most common answer I get is "I'm really frustrated with Excel and Prism, so I tried learning R but it was really complicated and I never got far enough to where I could apply it to my research." I made this course for them, and I hope you will like it too.

From the initial stages of quickly determining what your data is telling you, up to polished, publication-quality plots, this course will show you how to set up a smooth system for every step along the way.

It will save you time by automating your data analysis, so you can focus on designing experiments and interpreting the results for your next big paper.

Recently it has become more necessary for biologists to know some computational skills, but that doesn’t mean you have to be a programmer. My goal with this course is to give you an awesome introduction to the one skill that is immediately applicable to your research and also the easiest to learn right away. No matter what research you do, you will need to make some plots, and R is a great language for doing that. The best parts of R are the awesome packages that other people have built already. My favorites are ggplot and ComplexHeatmaps, so I go into detail on them in this course.

This video course will get you analyzing your data and plotting it quickly while teaching you only the programming skills that are most useful for your research, so you can stop messing around in Excel and get back to the fun part of your research.

Here's what I'll teach you.

Lesson 1: Hit the ground running — From data to plot with a few magic words

Lesson 2: Importing and downloading data — From Excel, text files, or publicly available data, I’ve got you covered.

Lesson 3: Interrogating your data — What are you???

Lesson 4: Filtering and cleaning up data — Kicking out the data that annoys you and polishing up the rest

Lesson 5: Tweaking everything in your plots — Satisfying your inner perfectionist…or the journal’s nit-picky demands…

Lesson 6: Plot anything! — A nice figure for any occasion

- Bar plots

- Scatter plots

- Box plots

- Violin plots

- Density plots

- Dot-plots

- Line-plots for time-course data

- Venn diagrams

Lesson 7: Multifaceted figures — When you just really need 92 plots to make your point

Lesson 8: Heatmaps — It’s gettin’ hot in here!

These lessons are a total of 3 hours of video content and all the code and data so you can follow along and play with the plots yourself.

By the end of this course, you will be able to confidently get your data into R (including straight from Excel), analyze it, produce several types of publication-quality plots, and automatically save them for your next big paper.

We will look at genomic data, gene lists, time-course data, structural variants, and copy number data for heatmaps. After just 3 hours of video lessons, you will be able to do things that took me months to learn.

[안유선-zr]

Thank you so much for sharing! It was awesome to learn R especially a beginner like me. I will enjoy watching all lessons! Thank you again!!

[setarehsohail]

I appreciate your hardworking and nice teaching method!

[mianadnankakakhel]

This is quite awesome. Thank you. kindly share a link to your lecture regarding barplot

[researcher]

Thank you so much ... you explained everything very clearly..just love it.

[bimpannapa]

Thank you so much for the great lessons. Your tutorials make me survive during lockdown. 😀

[GregThatcher]

Great video! Please make more videos showing such _practical_ and useful R examples.

[phyvijay]

Super helpful .. Easy steps to download the data files.. Million thanks ..

[taibiahmed]

Hello, thank you for this video first of all, I want ask you if you don't mind, . How can we have the plot with all max value in the bottom-left ?

[fabianabrandaoalvessilva]

greating feom Brazil. I wiil try this wonderful class on my Mac using R studio today. I've just started to learn R in a couple days, hope to get it

[raymon]

great video, but can i ask about how use Rstudio for fisheries?

[AmanUllah-tkwt]

Please be kind enough and make the dataset used in the video publicly available. I was unable to download @Maria Nattestad

[wendouble]

Oh，the files about code and scripts you uploaded before were invaild，could you upload again？ Good thanks for you！！

[sunilranjanroysamantasingh]

I exactly did what you have done but My bar graph doesn't contain color. Can you please help?

[mostafarahman]

could you please run the script for beysain netwrok in R

[human]

thanks a lot, that is a very helpful video.

[anilbhattarai]

Column 1 is self generated so i marked ?, and my actual values are in Temperature, and Year Column.
? Temperature Year
1 2.12771 1991
2 3.47961 1992
and so on till 2010. My table looks like this. I want simple barplot. Now using following code
~ name_of_dataframe$Temperature, data = yy) instead of showing year in x-axis it shows 1, 2, and so on with corresponding values of temperature in Y- axis. Could you help me to get the year in x-axis with xlim = c(1991, 2010)
Thanks in advance. :-)

[enhncr]

Using homygot.... vim + R is the way to go