Beautiful and customizable RNAseq volcano plots
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- Опубликовано: 12 июл 2024
- Color, size, and shape: I make a volcano plot of differentially expressed genes with and change the point colors, shapes, and sizes in Python. You will also see examples of pandas and matplotlib.
Notebook/DE csv:
github.com/mousepixels/sanbom...
github.com/mousepixels/sanbom...
0:00 Intro
0:23 Setup
1:56 Color
4:03 Shape
5:43 Size
6:43 Label genes
8:15 Beautify 
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this is amazing, your tutorials are so helpful!!
Thanks for your work. It's really useful.
Keep going with this channel, really useful tutorials ;)
Thank you! I have fun making the videos, so I plan to keep going at least for the foreseeable future!
@@sanbomics yeah, good thing is that python-based analysis is kinda a key topic, super cool!
Cannot be happier .
Really one more high quality education video
Can u tell me the packages i have to learn to much in python to do data wrangling confortably?
- can u make a video about NMF on single cell genomics data and how to visualize the programs of it ?
Anthe big like share and subscripe ❤️❤️❤️ keep going with this channel you make high quality education on it .
pandas is one of the most important packages. Moreover, because tools like scanpy and adata utilize pandas heavily. It's typically a must know for doing any sort of data analysis in python. numpy is also very important, especially if you are working with matrices. For visualization, seaborn and matplotlib are important. I may get around to a video like that in the future!
Thank you! ❤️
This is very helpful! Thank you for sharing!! :)
No problem! Glad it helped!
Great video! Thanks!
No problem! Thank you!
great tutorial !!
Thank you!!
Men U R a real hero
No you are the real hero! (The Boys reference)
Thanks for another good video.
I have a question; in bioinformatics projects, one of the main challenges is to tailor the data for the project and data interpretation. That would be great if you bring up the data like this and explain the best approach to deal with that.
No problem! I agree, it is always important to keep in mind the downstream analysis when you are designing a project. Even though I spend 95% of my time writing code, I actually am a hybrid scientist. I try to design my wet lab experiments to best address what I am trying to answer algorithmically. I can try to incorporate more of the project design in a future, longer video. Thanks for your input again!
Thanks for the lecture! Is there a way to pass marker edge color to hue instead of marker face color and parallelly set marker face color to 'none'?
You are going to have to modify the source code. Unfortunately, I didn't add that as an option
Great tutorial ! thankyou I just have small question if I want to highlight specific gene lists instead of random where can I insert them? Thanks again !
Hi! The random was just a way to generate an example list. Just input you list in the same spot instead of the random one.
@@sanbomics Thankyou !
Hi, thanks for the great video. It would be great to know customized label
Hi! What were you trying to customize? You can change the text properties directly in this line:
texts.append(plt.text(x = df.iloc[i].log2FoldChange, y = df.iloc[i].nlog10, s = df.iloc[i].symbol,
fontsize = 12, weight = 'bold'))
there are additional things you can change: matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.text.html
Let me know if this helps!
@@sanbomics Hi, thanks for your reply. I want to label list of selected genes.
Put that line of code above in an if statement. For example:
(and remove the filters that you don't want that I added for lfc/pvalue)
if df.iloc[i].symbol in my_list:
..... that line of code
@@sanbomics Thanks a lot for your reply
very useful, thank you! Is there a way to set axes limits?
Yup!. plt.xlim(right = ?, left = ?) top/bot for plt.ylim