Unable to run doLeidenCluster

[kendrix10]

Hi there,

I'm having some trouble running doLeidenCluster() function on my giotto_object. I've been following the Nanostring_cosmx_lung_cancer (4.0.3) workflow step-by-step, but I can't seem to figure out what went wrong with this error. Could you help me with this error please?

giotto_object <- doLeidenCluster(gobject = giotto_object, resolution = 1, n_iterations = 1000) ..

Error Message

```r Error: x.cell_ID is type environment which is not supported by data.table join ```

To Reproduce

I've followed the steps line-by-line and I kept encountering this issue even though I reloaded my session clean and re-rerun everything from top-down.

These are the processing steps that have been completed: Processing steps: 0_subset 1_filter name info: tag tag 2_normalize 3_normalize 4_normalize 5_feat_stats 6_cell_stats 7_feat_stats 8_cell_stats 9_hvf name info: hvf HVFplot 10_pca 11_umap 12_umap 13_umap 14_umap 15_nn_network 16_nn_network

Expected behavior

I expected the function to identify my cell clusters, so without it, it's a little difficult for me to proceed with my analysis.

Screenshots Here is a screenshot of the traceback of the error:

System Information

Please replace the following according to your machine:

• OS: macOS Sonoma 14.3.1
• Version [e.g. 4.0.1]
  • R version 4.3.2 (2023-10-31)
  • Giotto version 4.0.3
  • Python version 3.10.10

[kendrix10]

Fixed with #184