Open jonathjd opened 3 weeks ago
Hi @jonathjd, great suggestion!
I probably won't be able to implement this myself, but I'd love to help you open a PR.
This could be a method of the DeseqDataSet
class wrapping a function in utils.py
, similarly to plot_dispersions
in DeseqDataSet
which calls make_scatter
from utils
.
Let me know if you need any help :).
@BorisMuzellec That sounds like a great idea, and I would be happy to work on it! Let me know what I need to do to make it happen.
Is your feature request related to a problem? Please describe.
Right now there is no method that plots an RLE plot even though the
DeseqDataSet
method has both the normalized counts (DeseqDataSet.layers["norm_counts"]
) and estimated size factors (DeseqDataSet.obsm["size_factors"]
). RLE plots are useful for identifying technical variation and normalization issues in RNA-Seq data, as well as testing out different normalization strategies. These plots are super helpful in assessing and visualizing unwanted technical noise or batch effects in expression data.Describe the solution you'd like I propose implementing an RLE plot method, similar to the
plotRLE
function in EDASeq for R. The plot would display boxplots of the relative log expression of genes for each sample, centered around the median per gene. The implementation would:Describe alternatives you've considered
The implementation in other standard libraries (pandas, numpy, matplotlib) is not too bad, but it would be super handy if it came standard!
Additional context Here's an example of an RLE plot I've made that could be similar. Thanks!!