Adding spatial_exp_to_mif and error handling

[cansavvy]

Summary

• The spatial_exp_to_mif() function takes a spatialExperiment object and preps it to be a mif. The big caveat to this is I can't find more spatialExperiment objects thata re publicly available to test this on. So we will just have to adjust when that happens at some point.
• For the purposes of the workshop I also altered the example data to have clean_names(). However this did have a ripple effect in the code so the reason you will see so many files changed is that I had to change references to columns in code. I did this with a search and replace.

Testing

This was tested by running

devtools::check()

Which built the vignettes and examples which all passed.

Usage

# Create mif object
if (!("VectraPolarisData" %in% installed.packages())) {
BiocManager::install("VectraPolarisData")
}
ovarian <- VectraPolarisData::HumanOvarianCancerVP()

ova_mif <- spatial_exp_to_mif(spatial_exp = ovarian, 
                              patient_id = "sample_id",
                              markers = c("phenotype_cd68", "phenotype_cd3", "phenotype_cd8"))

[cansavvy]

Once I find where these example data are, we could just make it so they are ready to go instead of having these coerce mutates in the tutorial.

[cansavvy]

There is one note that the examples take too long to run. Just FYI.

   Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
   spatial_exp_to_mif 68.205  8.648  90.105
   NN_G                5.609  2.894   5.274
✔  checking for unstated dependencies in ‘tests’ (361ms)
─  checking tests (697ms)
    [83s/97s] OKthat.R’
   * checking for unstated dependencies in vignettes ... OK
   * checking package vignettes ... OK
   * checking re-building of vignette outputs ... [7m/12m] OK
   * checking for non-standard things in the check directory ... OK
   * checking for detritus in the temp directory ... OK
   * DONE
   
   Status: 1 NOTE
   See
     ‘/private/var/folders/2d/d8927cd105550jjcy7qy99_w0000gn/T/Rtmp3izT5s/file8f54e04e86b/spatialTIME.Rcheck/00check.log’
   for details.
   
── R CMD check results ──────────────────────────── spatialTIME 1.3.4-5 ────
Duration: 18m 26.7s

❯ checking for future file timestamps ... NOTE
  unable to verify current time

0 errors ✔ | 0 warnings ✔ | 1 note ✖