Improvements based on reviewers comments

dimalvovs commented 2 months ago

Here is the reviewer's comment:

The provided source code does not include any documentation regarding how should the code by used, in what order, under which software requirements and includes hardcoded paths to the authors' machine, making it unusable and hard to scrutinize. Improving the code would enable reproduction of the results and broad use of the analytical approach since the paper is mainly about bringing forth a new apporoach. Furthermore, I would recommend also depositing the source code in a openly accessibly, independent repository for archival such as Zenodo, which can be done easily by connecting the Github repositorie(s) to Zenodo.

Code documentation improvements

[ ] Vignettes?

visium analysis scripts

xenium analysis scripts

[x] do we need to store these comments? https://github.com/FertigLab/PanIN_carcinogeneisis_spatial_analysis/blob/52f6c9c010ff116490510f4d1a834567cbc0198e/scripts/xenium_analysis/01_Load_Xenium_Data.Rmd#L13
[x] should we export the conda env to allow reproducing with the same package versions?https://github.com/FertigLab/PanIN_carcinogeneisis_spatial_analysis/blob/52f6c9c010ff116490510f4d1a834567cbc0198e/scripts/xenium_analysis/01_Load_Xenium_Data.Rmd#L23
[x] if we use conda_env, do we need to specify the lib loc? https://github.com/FertigLab/PanIN_carcinogeneisis_spatial_analysis/blob/52f6c9c010ff116490510f4d1a834567cbc0198e/scripts/xenium_analysis/01_Load_Xenium_Data.Rmd#L18

closing

[ ] archive the version in Zenodo

jmitchell81 commented 2 months ago

Xenium comments addressed in d17a538. The conda environment usage is removed because it was a holdover from an initial attempt to use Leiden clustering. The presented scripts use Louvain clustering.

jmitchell81 commented 2 months ago

Commented out code removed in 091299b

FertigLab / PanIN_carcinogeneisis_spatial_analysis