Date; 2023/05/13

Recently, I have basically used scanpy for analysis of single cell RNA sequence because I need to use scVelo for RNA velocity analysis. Reason why I chose scanpy rather than Serurat is that scanpy and scVelo have really good compatibility. If you well know pandas and numpy, I confidentially say you are more comfortable with scanpy. I feel AnnData object is very easily to be understand their data structure and it can be handled with pandas and numpy.

I know a lot of persons are using jupyter on VScode and I am using those software too. Actually, I tried to use Spyder at first, but my Ubuntu circumstance (spyder on Ubuntu) did not accept jupyter-notebook from conda. So, I am using VScode for scanpy.

What things happened when I opened the VScode to continue my work is markdown and output area of VScode turned all grey color and I could not read anything and the all figures were masked as grey color.

In this blog, I record how to recover filling grey color on markdown and output area of VScode. To be honest, I don’t know what I did was correct way to recover from this problem, but It recovered to normal.

Masking grey color on markdown and output are of VScode

Anyway, I have used scanpy recently, and I ran into a trouble using VScode. See the image as below.

I think you can find the markdown and output area is turning grey color. It makes impossible to read anything other than code. If it can not be recovered, I can not do anything. It is totally super annoying for everybody.

I also felt bxxxxhit, assumed that cahe of VScode is full, and I started to google to find the way to recover it. However, I could not find good answer on the internet.

What I did at first and it can not fix it

At first, I run following command. These command was totally useless to recover by VScode.

1. Press “Control”, “Shift”, and “P” to open Command Palette
2. Clear Command history
3. Clear Editor History
4. Clear cache and Reload Window

And It did not fix this annoying error. I remember I spent several hours to battle this trouble, I lost several hours of my day. Usually, “Clear Cache and Reload WIndow” may solve this problem, but it can not in this case.

Delete every cache directory of VScode

I snapped to VScode, and then I decided to delete every possible cache directory of VScode. I do not expect what will be happened next, but if did not do it then I probably have been lost control of my mind, and destroy everything.

What I did at second was following.

rm -fR .config/Code/Cache
rm -fR .config/Code/CachedData
rm -fR .config/Code/'Local Storage'

Fortunately, it worked. After deleting cache directory of VScode, I restarted the software, and then I found markdown and output area turned normal.

However, all output before deleting cache looked gone, I mean, results such as uMAP and heatmap had been cleared. Therefore, if you tried it, then you need to run the code again.