deweylab / cell-type-classification-paper Goto Github PK

Hello,

I am currently doing my bachelor thesis with the goal of preventing the repeated retraining of the tool you have developed for cell classification - CellO - using some imputation methods. I am having some issues reproducing the results of the paper using the code of the evaluation you have provided for testing CellO on Zheng_PBMC, the lung cancer and the non-droplet datasets (i.e. to get the F1-scores and avg. precision for these datasets).

I downloaded the whole datasets from https://zenodo.org/record/4289064#.YoOS-FTP2Uk and the repository for running the evaluation from https://github.com/deweylab/cell-type-classification-paper.git. However, I could not understand how the code in the cell-type-classification-paper.git relates to the datasets files. In the Snakefiles there are some files required as an input or referenced.
I would have thought they could be found in the datasets files but they are not or are named differently. As an example, I could find bulk_labels.json in the dataset, but only references to labels.json in the code. There are references to expriment_to_study.json or untampered_bulk_primary_cells_with_data which I was also unable to identify.

I was also unsure which python scripts in the cell-type-classification-paper.git repository to run first. I would have thought to run the train_model.py first but as mentioned it required the labels.json and experiment_to_study.jsons files that do not exist in the provided datasets files.

Thus I would be grateful if you could help me with the following issues:

1. Which scripts should be run in order to reproduce the evaluation on the above mentioned three datasets?

2. In one of the python scripts in the cell-type-classification-paper.git repository, I found a dictionary for mapping the cell labels used by Zheng_PBMC dataset into the Cell Ontology labels. However, I could not find similar mapping dictionaries for the lung cancer and the non-droplet datasets. Do these exist? If so, I would be very gratful to get the cell types mapping for the remaining two datasets.

3. I tried to run CellO on the Zheng_PBMC.h5 from a jupyter notbook but it did not work because CellO expected it to be an AnnData (h5ad file). When I run it with command line it worked. Do you have any advice on how to use files with fomats other than h5ad format from jupyter notebook?

I would be very thankful for a quick response.