Easy RNAseq volcano plot with one line of code
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- Опубликовано: 13 ноя 2022
- Make a super easy and PRETTY volcano plot from differentially expressed genes with only one line of code. Plotting aesthetic figures can be challenging and/or time consuming. Here I show you how to make a pretty volcano plot without needed much prior coding knowledge. They are also highly customizable for more advanced users.
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I really needed this yesterday.. Thanks to you, I can see comfortable results.
Well I am sure you will be needing to make another volcano plot sometime soon! xD
That was just the epic first 10 seconds... What a stunning..!👏
Thank you so much 😀
Very nice, will be using this for sure. Keep up the good videos!
Will do! Thanks!
Bro, what? So cool to create a package that's based on your channels name! You're insane bro, in a good way! I guess I gotta long way to get to your level😅. Congratulations Broski!
haha thanks! You'll be there one day. I can still remember the days I didn't know what I was doing.
Brilliant! I'm looking forward to the package converting Ensemble IDs to Gene symbols.
Should be releasing it this week!
Simply woww..
pretty outstanding....!
Thank you!
amazing! So cool!
Thanks!!
This is quite helpful. Thank you
You're welcome!
@@sanbomics Do you have a function in the package that can be used to change the colors of differentially expressed genes?
Yup! you should be able to pass a color dictionary. color + list of genes. Check the docstring
@@sanbomics Cool, thanks so much
Amazing..
Thanks :)
Hi, how do I alter the scale on your Y and X axis? :) Great video btw
No way to do it right now.. will be making it more customizable in the future.
Thank you for the amazing tool, I just have 2 questions: 1: How to add a title to the plot, and 2: is there a possibility to change the names DE and not DE?
You can if you pass dictionaries of which to label. But this is a little involved. I plan to change it in the future to allow a little more flexibility. Right now, it may just be better to edit them afterwards in something like illustrator or powerpoint
What word does DE stand for? Can it be changed to significant change and non-significant change?
differentially expressed or differential expression. The genes that are DE will depend on the thresholds you use. Typically we use a corrected p-value < 0.05, so your DE genes at a minimum should be statistically significant.
@@sanbomics Thank you!
Just one question, if you simply want unregulated genes in red and down regulated genes in blue, how should I write the code? 😅
You can pass the upregulated genes and downregulated genes as a dictionary to the color_dict. Just grab their ids from the dataframe. It will look something like {'upregulated': the_up_genes, 'downregulated': the_down_genes}
you will also have to change the argument with the color order too
May I ask how can you change the argument with color order so that I could specify which group to be in which color?
@vjsanchezarevalo did you manage to customize the color based on the upregulated and downregulated genes. I need some guidance please.
haii may I know if it runs .tsv file?
if you import the tsv first as a pandas dataframe