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 ✖

[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 ✖

[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 ✖

[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 ✖

[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 ✖

[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 ✖

[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 ✖

[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 ✖