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drieslab / Giotto

Spatial omics analysis toolbox
https://drieslab.github.io/Giotto_website/
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giottoToSeurat states that "argument is of length zero" #668

Open acjordan333 opened 1 year ago

acjordan333 commented 1 year ago

Hello Giotto team,

Thanks so much again for making this tool. Sorry for posting another issue in such a short time frame. This tool is excellent and it's been very helpful in analyzing my NanoString CosMx data.

I have been trying to convert a Giotto object (created successfully using CosMx data) into a Seurat object so I can utilize the analysis tools in the Seurat pipeline. I try to do so using this code, pasted below:

seurat_0048 = giottoToSeurat(fov_join_all, spat_unit = "cell")

However, this error appears:

'Warning: Keys should be one or more alphanumeric characters followed by an underscore, setting key from negprobe to negprobe_Error in if (nrow(avail_dr) > 0) { : argument is of length zero'

My guess is there could be an issue with the way my Giotto object is structured. I called the object into the R console to get the specs of my giotto object (titled "fov_join_all"), which are as follows:

fov_join_all An object of class giotto Active spat_unit: cell Active feat_type: rna [SUBCELLULAR INFO] polygons : cell features : rna neg_probe [AGGREGATE INFO] expression ----------------------- [cell][rna] raw normalized scaled pearson [cell][neg_probe] raw normalized scaled spatial locations ---------------- [cell] raw spatial networks ----------------- [cell] Delaunay_network dim reduction -------------------- [cell][rna] pca umap nearest neighbor networks -------- [cell][rna] sNN.pca attached images ------------------ giottoLargeImage : 20 items... giottoLargeImage : 20 items...

My specs are as follows:

R version 4.2.2 Giotto version 3.3.0 macOS Ventura 13.2

Thanks for your help. Let me know if you need more specifics on the issue.

acjordan333 commented 1 year ago

Hi Giotto team,

Thanks so much for working on this issue! I wanted to ask if there are any updates on this or if any of you have seen anything like this happen before. I'd like to see if there's something I could potentially be executing incorrectly as I try to convert a giotto object into a Seurat object.