I recently read your article published in Nature Methods titled "Benchmarking spatial clustering methods with spatially resolved transcriptomics data" and found it deeply inspiring. However, I encountered some issues while trying to replicate the SpaceFlow-DC results, and I am hoping you might offer some guidance.
Issue Description
When I input each sample into the SpaceFlow algorithm, the resulting embeddings visualizations closely resemble those in Figure 5a of your article (as shown in Figures 1-3 below). However, I face difficulties achieving the results depicted in Figure 5b of your paper (as shown in Figures 4-5 below) when using the Harmony alignment.
Request for Assistance
Could you possibly provide the code used to generate Figure 5b, or could you advise on the Harmony parameters that might help in reproducing these results? Any assistance you could provide would be greatly appreciated.
I recently read your article published in Nature Methods titled "Benchmarking spatial clustering methods with spatially resolved transcriptomics data" and found it deeply inspiring. However, I encountered some issues while trying to replicate the SpaceFlow-DC results, and I am hoping you might offer some guidance.
Issue Description When I input each sample into the SpaceFlow algorithm, the resulting embeddings visualizations closely resemble those in Figure 5a of your article (as shown in Figures 1-3 below). However, I face difficulties achieving the results depicted in Figure 5b of your paper (as shown in Figures 4-5 below) when using the Harmony alignment.
Request for Assistance Could you possibly provide the code used to generate Figure 5b, or could you advise on the Harmony parameters that might help in reproducing these results? Any assistance you could provide would be greatly appreciated.
Thank you for your time and consideration.