Hello Bioinformatics lovers,

Happy Holidays! We had a big snow in Boston.

Early in the morning, my in-law told me our neighbor was helping us to remove the snow using a gas snow blower.

I went out and said thanks. He told me that he liked helping others.

I can tell the pure JOY from his words.

Helping others is helping yourself.

“Giving roses to others leaves fragrance on your hands.”

Enough for the life-lessons :)

How are you going to spend the holidays? For me,

I am writing the end-to-end tutorial to replicate the figure below, which I mentioned in my last newsletter.

Read it if you missed it https://divingintogeneticsandgenomics.kit.com/posts/good-to-great-bioinformatician-how​

To be able to do it, you first need to master the basic skill: plotting!

If you master these six types of plots you can reproduce 90% of the figures in any genomics paper.

1. barplot
2. scatterplot
3. histogram
4. line plot
5. boxplot
6. heatmap

​

Watch the video here:

I did not include others such as Venn diagram, or pie chart. But you get the idea.

Looking at this figure,

• figure d is a scatter plot,
• figures e, f and k are (stacked) bar plot
• g is a IGV genome browser view of ChIPseq signal, but it is really just a histogram.
• h is a pie chart
• i is a heatmap
• j is a line plot

I still use ggplot2 for most of my figures and use complexheatmap for making heatmaps.

If you do want to stay within the ggplot2 ecosystem, take a look at ggalign.​

It can make complicated heatmaps using ggplot2:

compare it with complexheatmap​

Okay, that's the first step. I highly recommend you go through the following free books:

• R Graphics Cookbook, 2nd edition https://r-graphics.org/​
• Data visualization A practical introduction https://socviz.co/

Then, you need to learn how to pre-process the underlying sequencing data. In this case, ChIP-seq;

analyze the figures and see what is needed to plot them;

get the data into a dataframe that is ready for you to plot.

I will show you how to do it all!

Wish me good luck with the writing.

Happy Learning!

Tommy aka. Crazyhottommy

PS:

If you want to learn Bioinformatics, there are ways that I can help:

1. My free YouTube Chatomics channel, make sure you subscribe to it.
2. I have many resources collected on my github here.
3. I have been writing blog posts for over 10 years https://divingintogeneticsandgenomics.com/​

Stay awesome!