Missing file "utils.py"

[hjames1]

Hello, thanks for sharing.

However, the "utils.py" file which contains "bean_plot" function is not included in the folder.

By the way, the following files do not seem to be uploaded successfully.

correlation.py
cluster.py
add-tme.py
visualize-tme.py
corrsearch.py
funcs.py
utils.py
convert-to-loompy.py
update-files.py
update-namemap.py

Can you check? Thanks.

[almaan]

Hello @hjames1, thank you for your comment and making me aware of this. It seems like I accidentally added the utils.py file to the .gitignore file - this is now taken care of utils.py is a part of the repo.

I don't think the other files you list are used for any of the analyses in the manuscript, but rather represent ideas that we chose to not pursue any further. I could share them of course, but don't want to make the repo cluttered with things that aren't relevant. However, I could put them up on a different branch if you're really keen to access them, is there a particular reason as to why you request these files as well?

Best, Alma

[hjames1]

Thanks for your quick reply! If other documents are not relevant to the manuscript, then I don't need them.

[hjames1]

By the way, some other files generated by stereoscope are also missing (^W files in./res/ST-deconv/props)

Can you check please ?

[almaan]

@hjames1 , which proportion files are missing? As far as I can see the zip files containing the proportion estimates of all cell types are there. These files are, for clarity, no longer named W*tsv but rather [patient][section]-proportion.tsv and are found in the aforementioned zip files (named: major.zip, minor.zip, and subset.zip.

Best, Alma

[hjames1]

@almaan , thanks a lot, now corrplot.r script is now running smoothly according to your hints.

[almaan]

@hjames1 , great - if you feel as if your questions have been answered, feel free to close this issue :)

[hjames1]

@almaan OK, I'll close this issue :)