Full datasets - Githubissues

ndamond commented 2 years ago

As suggested by @lassedochreden (https://github.com/BodenmillerGroup/imcdatasets/issues/21), imcdatasets should give the option to retrieve full single cell data.

Context Due to memory space limitations it is not possible to load all multichannel images for the Breast cancer and Pancreas datasets. For this reason, imcdatasets only provides a subset of images (100 per dataset) and the associated single cell data and cell segmentation masks.

Goal Provide full single cell data and cell segmentation masks for the Breast cancer (JacksonFischer_2020_BreastCancer) and Pancreas (Damond_2019_Pancreas) datasets.

Things to implement

[x] Provide full single cell data, including the Zurich cohort, for the Breast cancer dataset.
[x] Provide all cell masks for the Breast cancer dataset.
[x] Provide a matched image/masks/single-cell subsetted dataset of the Zurich cohort for the Breast cancer dataset (as it already exists for the Basel cohort).
[x] Provide full single cell data for the Pancreas dataset.
[x] Provide all cell masks for the Pancreas dataset.
[x] Upload new data objects to ExperimentHub.
[x] Update loading functions and documentation.

ndamond commented 1 year ago

Hi @lassedochreden,

The full datasets have been uploaded to ExperimentHub, would you mind testing the updated functions?

You can install this branch with devtools::install_github("https://github.com/BodenmillerGroup/imcdatasets/tree/full_datasets") (requires BioC v3.17).

Thanks!

lassedochreden commented 1 year ago

Hi @ndamond,

if I am not mistaken the current (not devel) version of BioC is 3.16 (https://www.bioconductor.org/install/), right?

I have tested following call: sce <- imcdatasets::JacksonFischer_2020_BreastCancer(data_type = "sce", full_dataset = TRUE)

and get following error: snapshotDate(): 2022-10-31 Error in .local(x, i, j = j, ...) : 'i' must be length 1

Thanks for looking into it! :)

SessionInfo:


Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8        LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8    LC_PAPER=C.UTF-8       LC_NAME=C             
 [9] LC_ADDRESS=C           LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] imcdatasets_1.7.1           cytomapper_1.10.1           EBImage_4.40.0              SpatialExperiment_1.8.0     SingleCellExperiment_1.20.0 SummarizedExperiment_1.28.0
 [7] Biobase_2.58.0              GenomicRanges_1.50.2        GenomeInfoDb_1.34.7         IRanges_2.32.0              S4Vectors_0.36.1            BiocGenerics_0.44.0        
[13] MatrixGenerics_1.10.0       matrixStats_0.63.0         

loaded via a namespace (and not attached):
  [1] AnnotationHub_3.6.0           BiocFileCache_2.6.0           systemfonts_1.0.4             sp_1.6-0                      shinydashboard_0.7.2          BiocParallel_1.32.5          
  [7] usethis_2.1.6                 ggplot2_3.4.0                 digest_0.6.31                 htmltools_0.5.4               viridis_0.6.2                 magick_2.7.3                 
 [13] tiff_0.1-11                   fansi_1.0.4                   magrittr_2.0.3                memoise_2.0.1                 limma_3.54.1                  remotes_2.4.2                
 [19] Biostrings_2.66.0             svgPanZoom_0.3.4              R.utils_2.12.2                svglite_2.1.1                 prettyunits_1.1.1             jpeg_0.1-10                  
 [25] colorspace_2.1-0              blob_1.2.3                    rappdirs_0.3.3                dplyr_1.1.0                   callr_3.7.0                   crayon_1.5.2                 
 [31] RCurl_1.98-1.10               glue_1.6.2                    gtable_0.3.1                  nnls_1.4                      zlibbioc_1.44.0               XVector_0.38.0               
 [37] DelayedArray_0.24.0           pkgbuild_1.3.1                DropletUtils_1.18.1           Rhdf5lib_1.20.0               HDF5Array_1.26.0              abind_1.4-5                  
 [43] scales_1.2.1                  DBI_1.1.3                     edgeR_3.40.2                  Rcpp_1.0.10                   viridisLite_0.4.1             xtable_1.8-4                 
 [49] dqrng_0.3.0                   bit_4.0.5                     htmlwidgets_1.6.1             httr_1.4.4                    RColorBrewer_1.1-3            ellipsis_0.3.2               
 [55] pkgconfig_2.0.3               R.methodsS3_1.8.2             scuttle_1.8.4                 dbplyr_2.3.0                  locfit_1.5-9.7                utf8_1.2.3                   
 [61] tidyselect_1.2.0              rlang_1.0.6                   later_1.3.0                   AnnotationDbi_1.60.0          munsell_0.5.0                 BiocVersion_3.16.0           
 [67] tools_4.2.0                   cachem_1.0.6                  cli_3.6.0                     generics_0.1.3                RSQLite_2.2.20                ExperimentHub_2.6.0          
 [73] devtools_2.4.3                fastmap_1.1.0                 fftwtools_0.9-11              yaml_2.3.7                    processx_3.6.1                bit64_4.0.5                  
 [79] fs_1.6.0                      purrr_1.0.1                   KEGGREST_1.38.0               sparseMatrixStats_1.10.0      mime_0.12                     R.oo_1.25.0                  
 [85] compiler_4.2.0                rstudioapi_0.14               beeswarm_0.4.0                filelock_1.0.2                curl_5.0.0                    png_0.1-8                    
 [91] interactiveDisplayBase_1.36.0 tibble_3.1.8                  ps_1.7.2                      lattice_0.20-45               Matrix_1.5-1                  vctrs_0.5.2                  
 [97] pillar_1.8.1                  lifecycle_1.0.3               rhdf5filters_1.10.0           BiocManager_1.30.19           bitops_1.0-7                  raster_3.6-14                
[103] httpuv_1.6.8                  R6_2.5.1                      promises_1.2.0.1              gridExtra_2.3                 vipor_0.4.5                   sessioninfo_1.2.2            
[109] codetools_0.2-18              assertthat_0.2.1              pkgload_1.3.0                 rhdf5_2.42.0                  rjson_0.2.21                  withr_2.5.0                  
[115] GenomeInfoDbData_1.2.9        parallel_4.2.0                terra_1.7-3                   grid_4.2.0                    beachmat_2.14.0               DelayedMatrixStats_1.20.0    
[121] shiny_1.7.4                   ggbeeswarm_0.7.1 ```

ndamond commented 1 year ago

Hi Lasse, Thanks for testing it.

All changes made to the package are applied to the development version, not the release, hence the 3.17 requirement.

It looks like you don't have the latest ExperimentHub snapshot version (snapshotDate(): 2022-10-31) so the new dataset is not found. They made a new build a few days ago (2023-01-30 I think) but it probably requires BioC 3.17.

BodenmillerGroup / imcdatasets

Full datasets #23