v1.1 bug fixes

[maddygriz]

• [x] resolves #47, customer found this issue when printing the SpatialPosition data. This can be tested using overlay(SOO_object). Printing shouldn't error.
• [x] resolves #48, add plotting factors should still work even if there are 2 columns with the sampNames to match on. This is fixed in both data.table and GeomxSet objects. Column with the most matches are used just to be safe. ADO issue
• [x] when saving xml file in xmlExtraction, file type changed to xml even if outDir is set.
• [x] ROI matching can occur on characters ADO issue
• [x] correct lab worksheet called in vignette and tests ADO issue
• [x] resolves #49, fixes overcropping on new fluorescence values

[maddygriz]

confirming tests work with devtools::test()

══ Results ════════ Duration: 136.9 s

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 421 ]

[mgrout81]

I took a look at all six items above and ran into problems with three of them.

Add plotting factor fix worked with GeoMxSet object as annot, but not witha df.

mouse <- "mu_dev_E11_005"
print(paste("Mouse is", mouse))

# Get lab worksheet to use with this mouse  
lw_fn <- all_lw %>% select(slide_name, lw_fn) %>% 
  unique() %>% filter(slide_name == mouse) %>% 
  select(lw_fn) %>% unlist()

tifFile <- dir("~/data/cwilliams/sfn2023_mouseembryo_geomx/image_files/", 
               pattern = paste0(mouse, ".ome.tiff"),
               full.names = TRUE, recursive = TRUE)

soo <- readSpatialOverlay(ometiff = tifFile, annots = lw_fn, 
                          slideName = mouse, image = TRUE, #TRUE  
                          saveFile = FALSE, outline = FALSE,
                          res = res)

unk <- annots %>% filter(claire_q == "?") %>% mutate(claire_q = roi)

addPlottingFactor(overlay = soo, annots = unk,
                     plottingFactor = "claire_q") %>% sampNames()
# incorrect output: character(0), and all ROIs not matched

xml Extraction:

tifFile <- "/home/rstudio/data/cwilliams/sfn2023_mouseembryo_geomx/image_files//mu_dev_E9_image_files/mu_dev_E9_001.ome.tiff"
d <- "~/data/mgrout/soo_v1.1_testing/ome-tiff-xml-output"
dir.create(d, showWarnings = FALSE)

xmlExtraction(tifFile, saveFile=TRUE, outdir = d)

list.files(d)
# incorrect output: [1] "mu_dev_E9_001.ome.tiff"

ROI character matching

list.files("~/data/mgrout/soo_v1.1_testing/paredes/")

lw_fn <- "~/data/mgrout/soo_v1.1_testing/paredes/GW23_1_Pilot_82522_Paredes_20220829T2254_LabWorksheet.txt"
ome_tiff_fn <- "~/data/mgrout/soo_v1.1_testing/paredes/GW23_1_Pilot_82522_Paredes.ome.tiff"

soo <- readSpatialOverlay(ometiff = ome_tiff_fn, annots = lw_fn, 
                          slideName = "GW23_1_Pilot_82522_Paredes", image = TRUE, #TRUE  
                          saveFile = FALSE, outline = FALSE,
                          res = res)

# Error, could not open:
# Extracting XML
# Parsing XML - scan metadata
# Parsing XML - overlay data
# Error in if (nrow(AOIattrs) < nrow(annots)) { : 
#     argument is of length zero
#   In addition: There were 48 warnings (use warnings() to see them)

[mgrout81]

Update: I'm also seeing issues with cropping using mu_dev_E15_012.ome.tiff. See settings in screenshot.

[maddygriz]

@mgrout81

• I didn't have a way to add a tibble factor to the SpatialOverlay object. Added that now, same as data.frame.
• Fixed xml saving
• It would help to have merged in the stringROInames fix. Merged that in and it should be ready now.

Will look at the cropping issue next.

[maddygriz]

I also added the capability to have the scale bar in mm instead of just um.

[mgrout81]

Scale bar issue: https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/commit/6389565765bb600ec002de45730aa80013899d57#r129172009 Works and looks good with um and mm, but not nm.

Using my own script and v1.1.1 of the repo, I couldn't re-create the issue I saw here:https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/pull/50#issuecomment-1734583862

The three issues I ran into in the above comment (https://github.com/Nanostring-Biostats/SpatialOmicsOverlay/pull/50#issuecomment-1734379257) are now working for me. The three items that were earlier working for me are still working.

[maddygriz]

longtests updated mostly updating slide name with new lab worksheet. Needed to update _snaps for vdiffr tests since annotations changed.

Confirmed normal tests still work.

[maddygriz]

── BiocCheck results ── 0 ERRORS | 2 WARNINGS | 8 NOTES warnings = package size and even number version

── longtests results── [ FAIL 0 | WARN 0 | SKIP 0 | PASS 725 ]

── devtools::check() results ──

── R CMD check results ────────────────────────────── SpatialOmicsOverlay 1.1.1 ────
Duration: 14m 38.9s

❯ checking for unstated dependencies in examples ... OK
   WARNING
  ‘qpdf’ is needed for checks on size reduction of PDFs

❯ checking DESCRIPTION meta-information ... NOTE
  License components which are templates and need '+ file LICENSE':
    MIT

❯ checking top-level files ... NOTE
  File
    LICENSE
  is not mentioned in the DESCRIPTION file.
  Non-standard files/directories found at top level:
    ‘longtests’ ‘reqs.md’ ‘specs.md’

❯ checking R code for possible problems ... [53s/33s] NOTE
  plotSpatialOverlay: no visible binding for global variable ‘xcoor’
  plotSpatialOverlay: no visible binding for global variable ‘ycoor’
  plotSpatialOverlay: no visible binding for global variable ‘sampleID’
  plotSpatialOverlay: no visible binding for global variable ‘Target’
  scaleBarPrinting: no visible binding for global variable ‘X’
  scaleBarPrinting: no visible binding for global variable ‘Y’
  Undefined global functions or variables:
    Target X Y sampleID xcoor ycoor

❯ checking for non-standard things in the check directory ... NOTE
  Found the following files/directories:
    ‘muBrainSubset_SpatialOverlay.RDS’ ‘muBrain_GxT.RDS’

0 errors ✔ | 1 warning ✖ | 4 notes ✖

── R CMD check results - expected error ──

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  pdflatex is not available
Error in running tools::texi2pdf()
You may want to clean up by 'rm -Rf /tmp/RtmpfanphI/Rd2pdf2b0b45340877'
* DONE

Status: 1 ERROR, 1 WARNING, 3 NOTEs