Entering edit mode
3.7 years ago
Hi,
I'm working on generating correlation matrixes for scRNA-seq dataset in Python using an algorithm called 'sceb' (Determining sequencing depth in a single-cell RNA-seq experiment). I've successfully made a correlation matrix from top 25 genes based on EB-estimated (Empirical Bayes estimators) Pearson correlation. However, when I tried to choose random genes to make a matrix, some genes with the correlation value 0 showed up and messed up the matrix.You can see some blanc areas in the matrix, I don't know how to fix it. Could you please give me some suggestions！ Thank you in advance! Yi
![enter image description here][1]
I don't agree with the statement that "the matrix is messed up", but if you don't like to see white squares for instances of zero, you can probably change the color scheme so that white isn't the color representing zero/the middle of your data range.
Since you didn't specify the code that you used to generate the heatmap it's a bit difficult to point you into the right direction though, Generally, the matplotlib color schemes can be seen here: https://scitools.org.uk/iris/docs/latest/_images/brewer.png -- you should pick one that obviously doesn't include white.