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title: "Interoperability with SpatialExperiment and AnnData"
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```{r, include = FALSE}
knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
library(cellspecR)
x <- cs_example()
policy <- cs_signal_policy(cs_markers(x))
```

The SpatialExperiment conversion keeps the selected signal as the main assay,
all raw measurements as an alternative experiment, and stores the images,
channels, provenance and policy in metadata.

```{r}
if (requireNamespace("SpatialExperiment", quietly = TRUE)) {
  spe <- cs_as_spe(x, policy)
  dim(spe)
  y <- cs_from_spe(spe)
  identical(cs_measurements(x), cs_measurements(y))
} else {
  message("Install SpatialExperiment to run this section.")
}
```

AnnData conversion is optional and requires an `anndataR` installation with a
working Python AnnData runtime.

```{r}
if (requireNamespace("anndataR", quietly = TRUE)) {
  result <- tryCatch(cs_as_anndata(x, policy), error = function(e) e)
  if (inherits(result, "error")) message(conditionMessage(result)) else result
} else {
  message("Install anndataR to run this section.")
}
```