Lambda Moses

The output does not match the standard output format of any commercial technology, unless you use Xenium Ranger to convert it and then use `readXenium`. The output includes the gene...

Regarding this error: ``` Error in wk_handle.wk_wkb(wkb, s2_geography_writer(oriented = oriented, : Loop 0 is not valid: Edge 34 crosses edge 36 In addition: Warning messages: 1: In st_is_longlat(x) : bounding...

The column name "cell_id" is just an example. Any name can be used, but there should be a column for cell IDs to match the cell metadata to the gene...

> Also, sf::st_read didnt work I think because I was trying to read the .gz file directly(?) I think it's probably because of the gz. Do cellmeta and segmentation have...

Me too, I have the same issue, especially when a few words appear way more often than other words and often those few most frequent words aren't all plotted.

It seems that it's trying to download Bio-Formats at this stage, which can take a while depending on your internet, and I got ``` Warning in utils::download.file(bf_url, bf_jar, mode =...

Sorry, didn't see this earlier. This package depends on the [`ochRe`](https://github.com/ropenscilabs/ochRe) R package, which is not on CRAN. What's the error message you got when trying to load this package?

Or maybe just another `ggplot` method for SFE, no separate functions for `plotSpatialFeature` and `plotLocalResult`. Those are just different fields of the SFE data, like glorified data frame columns. But...

Do you like Seurat's design with lots of arguments? Or do you find it confusing? I'd like to do better than Seurat. My problem here is the potential confusion when...

Maybe something like `plotSpatialFeature() + plotMolecules()`. Or maybe the kernel density heatmap can go into `imgData`, which `SpatialExperiment` authors probably didn't foresee. I can have it both ways, with both...