PeteHaitch
commented
1 year ago Hi @gartician,
Thank you making the changes to CITEViz following the pre-review comments. The interoperability with SingleCellExperiment requirement is great to have and, overall, I now find the app much simpler to try out and use.
For acceptance into Bioconductor, there are a number of Required points, as well as Recommended points, that I would ask you to first please address. Would you please provide line-by-line comments to my initial review so that I know what changes I'm looking for in my re-review.
Cheers, Pete
Required
- [ ] I had some problems when running the vignette for the first time. It seems the Seurat package has to be loaded before either ExperimentHub resource
EH7739(Seurat-formatted) orEH7740(SingleCellExperiment-format) can be loaded. That it causes problems even for the SingleCellExperiment-formatted object suggests it's a problem with the CITEVizTestData package.
# Error without Seurat loaded/attached.
suppressPackageStartupMessages(library(ExperimentHub))
eh <- ExperimentHub()
#> snapshotDate(): 2022-11-21
# Download and load the Seurat-formatted object.
eh[["EH7739"]]
#> see ?CITEVizTestData and browseVignettes('CITEVizTestData') for documentation
#> loading from cache
#> require("SeuratObject")
#> Loading required package: Seurat
#> Error: package or namespace load failed for 'Seurat' in .doLoadActions(where, attach):
#> error in load action .__A__.1 for package RcppAnnoy: loadModule(module = "AnnoyAngular", what = TRUE, env = ns, loadNow = TRUE): Unable to load module "AnnoyAngular": attempt to apply non-function
#> Error: failed to load resource
#> name: EH7739
#> title: CITEVizTestDataSeurat
#> reason: unable to find required package 'Seurat'Created on 2022-11-22 with reprex v2.0.2
Session info
``` r sessionInfo() #> R Under development (unstable) (2022-11-18 r83369) #> Platform: x86_64-apple-darwin17.0 (64-bit) #> Running under: macOS Big Sur ... 10.16 #> #> Matrix products: default #> BLAS: /Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libRblas.0.dylib #> LAPACK: /Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libRlapack.dylib #> #> locale: #> [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8 #> #> time zone: Australia/Melbourne #> tzcode source: internal #> #> attached base packages: #> [1] stats graphics grDevices utils datasets methods base #> #> other attached packages: #> [1] SeuratObject_4.1.3 sp_1.5-1 CITEVizTestData_0.99.4 #> [4] ExperimentHub_2.7.0 AnnotationHub_3.7.0 BiocFileCache_2.7.0 #> [7] dbplyr_2.2.1 BiocGenerics_0.45.0 #> #> loaded via a namespace (and not attached): #> [1] tidyselect_1.2.0 dplyr_1.0.10 #> [3] blob_1.2.3 filelock_1.0.2 #> [5] Biostrings_2.67.0 bitops_1.0-7 #> [7] fastmap_1.1.0 RCurl_1.98-1.9 #> [9] RANN_2.6.1 promises_1.2.0.1 #> [11] reprex_2.0.2 digest_0.6.30 #> [13] mime_0.12 lifecycle_1.0.3 #> [15] ellipsis_0.3.2 KEGGREST_1.39.0 #> [17] interactiveDisplayBase_1.37.0 RSQLite_2.2.18 #> [19] ROCR_1.0-11 magrittr_2.0.3 #> [21] compiler_4.3.0 rlang_1.0.6 #> [23] tools_4.3.0 utf8_1.2.2 #> [25] yaml_2.3.6 knitr_1.41 #> [27] bit_4.0.5 curl_4.3.3 #> [29] RColorBrewer_1.1-3 KernSmooth_2.23-20 #> [31] withr_2.5.0 purrr_0.3.5 #> [33] grid_4.3.0 stats4_4.3.0 #> [35] fansi_1.0.3 xtable_1.8-4 #> [37] future_1.29.0 progressr_0.11.0 #> [39] MASS_7.3-58.1 globals_0.16.2 #> [41] cli_3.4.1 rmarkdown_2.18 #> [43] crayon_1.5.2 generics_0.1.3 #> [45] future.apply_1.10.0 rstudioapi_0.14 #> [47] httr_1.4.4 DBI_1.1.3 #> [49] cachem_1.0.6 stringr_1.4.1 #> [51] zlibbioc_1.45.0 parallel_4.3.0 #> [53] assertthat_0.2.1 AnnotationDbi_1.61.0 #> [55] BiocManager_1.30.19 XVector_0.39.0 #> [57] vctrs_0.5.1 Matrix_1.5-3 #> [59] IRanges_2.33.0 S4Vectors_0.37.0 #> [61] bit64_4.0.5 listenv_0.8.0 #> [63] parallelly_1.32.1 glue_1.6.2 #> [65] codetools_0.2-18 stringi_1.7.8 #> [67] BiocVersion_3.17.1 later_1.3.0 #> [69] GenomeInfoDb_1.35.5 tibble_3.1.8 #> [71] pillar_1.8.1 rappdirs_0.3.3 #> [73] htmltools_0.5.3 GenomeInfoDbData_1.2.9 #> [75] R6_2.5.1 evaluate_0.18 #> [77] shiny_1.7.3 Biobase_2.59.0 #> [79] lattice_0.20-45 highr_0.9 #> [81] png_0.1-7 memoise_2.0.1 #> [83] httpuv_1.6.6 Rcpp_1.0.9 #> [85] xfun_0.35 fs_1.5.2 #> [87] pkgconfig_2.0.3 ```# Things work fine if Seurat is loaded/attached.
suppressPackageStartupMessages(library(ExperimentHub))
suppressPackageStartupMessages(library(Seurat))
eh <- ExperimentHub()
#> snapshotDate(): 2022-11-21
# Download and load the Seurat-formatted object.
eh[["EH7739"]]
#> see ?CITEVizTestData and browseVignettes('CITEVizTestData') for documentation
#> loading from cache
#> An object of class Seurat
#> 20957 features across 2500 samples within 2 assays
#> Active assay: SCT (20729 features, 5000 variable features)
#> 1 other assay present: ADT
#> 6 dimensional reductions calculated: apca, aumap, pca, spca, umap, wnn.umapCreated on 2022-11-22 with reprex v2.0.2
Session info
``` r sessionInfo() #> R Under development (unstable) (2022-11-18 r83369) #> Platform: x86_64-apple-darwin17.0 (64-bit) #> Running under: macOS Big Sur ... 10.16 #> #> Matrix products: default #> BLAS: /Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libRblas.0.dylib #> LAPACK: /Library/Frameworks/R.framework/Versions/4.3/Resources/lib/libRlapack.dylib #> #> locale: #> [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8 #> #> time zone: Australia/Melbourne #> tzcode source: internal #> #> attached base packages: #> [1] stats graphics grDevices utils datasets methods base #> #> other attached packages: #> [1] CITEVizTestData_0.99.4 SeuratObject_4.1.3 Seurat_4.3.0 #> [4] ExperimentHub_2.7.0 AnnotationHub_3.7.0 BiocFileCache_2.7.0 #> [7] dbplyr_2.2.1 BiocGenerics_0.45.0 #> #> loaded via a namespace (and not attached): #> [1] RColorBrewer_1.1-3 rstudioapi_0.14 #> [3] jsonlite_1.8.3 magrittr_2.0.3 #> [5] spatstat.utils_3.0-1 rmarkdown_2.18 #> [7] fs_1.5.2 zlibbioc_1.45.0 #> [9] vctrs_0.5.1 ROCR_1.0-11 #> [11] spatstat.explore_3.0-5 memoise_2.0.1 #> [13] RCurl_1.98-1.9 htmltools_0.5.3 #> [15] curl_4.3.3 sctransform_0.3.5 #> [17] parallelly_1.32.1 KernSmooth_2.23-20 #> [19] htmlwidgets_1.5.4 ica_1.0-3 #> [21] plyr_1.8.8 plotly_4.10.1 #> [23] zoo_1.8-11 cachem_1.0.6 #> [25] igraph_1.3.5 mime_0.12 #> [27] lifecycle_1.0.3 pkgconfig_2.0.3 #> [29] Matrix_1.5-3 R6_2.5.1 #> [31] fastmap_1.1.0 GenomeInfoDbData_1.2.9 #> [33] fitdistrplus_1.1-8 future_1.29.0 #> [35] shiny_1.7.3 digest_0.6.30 #> [37] colorspace_2.0-3 patchwork_1.1.2 #> [39] AnnotationDbi_1.61.0 S4Vectors_0.37.0 #> [41] tensor_1.5 irlba_2.3.5.1 #> [43] RSQLite_2.2.18 filelock_1.0.2 #> [45] progressr_0.11.0 spatstat.sparse_3.0-0 #> [47] fansi_1.0.3 polyclip_1.10-4 #> [49] abind_1.4-5 httr_1.4.4 #> [51] compiler_4.3.0 bit64_4.0.5 #> [53] withr_2.5.0 DBI_1.1.3 #> [55] highr_0.9 MASS_7.3-58.1 #> [57] rappdirs_0.3.3 tools_4.3.0 #> [59] lmtest_0.9-40 interactiveDisplayBase_1.37.0 #> [61] httpuv_1.6.6 future.apply_1.10.0 #> [63] goftest_1.2-3 glue_1.6.2 #> [65] nlme_3.1-160 promises_1.2.0.1 #> [67] grid_4.3.0 Rtsne_0.16 #> [69] reshape2_1.4.4 cluster_2.1.4 #> [71] generics_0.1.3 spatstat.data_3.0-0 #> [73] gtable_0.3.1 tidyr_1.2.1 #> [75] data.table_1.14.6 sp_1.5-1 #> [77] utf8_1.2.2 XVector_0.39.0 #> [79] spatstat.geom_3.0-3 RcppAnnoy_0.0.20 #> [81] ggrepel_0.9.2 RANN_2.6.1 #> [83] BiocVersion_3.17.1 pillar_1.8.1 #> [85] stringr_1.4.1 later_1.3.0 #> [87] splines_4.3.0 dplyr_1.0.10 #> [89] lattice_0.20-45 deldir_1.0-6 #> [91] survival_3.4-0 bit_4.0.5 #> [93] tidyselect_1.2.0 Biostrings_2.67.0 #> [95] miniUI_0.1.1.1 pbapply_1.6-0 #> [97] knitr_1.41 gridExtra_2.3 #> [99] IRanges_2.33.0 scattermore_0.8 #> [101] stats4_4.3.0 xfun_0.35 #> [103] Biobase_2.59.0 matrixStats_0.63.0 #> [105] stringi_1.7.8 lazyeval_0.2.2 #> [107] yaml_2.3.6 evaluate_0.18 #> [109] codetools_0.2-18 tibble_3.1.8 #> [111] BiocManager_1.30.19 cli_3.4.1 #> [113] uwot_0.1.14 xtable_1.8-4 #> [115] reticulate_1.26 munsell_0.5.0 #> [117] Rcpp_1.0.9 GenomeInfoDb_1.35.5 #> [119] spatstat.random_3.0-1 globals_0.16.2 #> [121] png_0.1-7 parallel_4.3.0 #> [123] ellipsis_0.3.2 ggplot2_3.4.0 #> [125] assertthat_0.2.1 blob_1.2.3 #> [127] reprex_2.0.2 bitops_1.0-7 #> [129] listenv_0.8.0 viridisLite_0.4.1 #> [131] scales_1.2.1 ggridges_0.5.4 #> [133] leiden_0.4.3 purrr_0.3.5 #> [135] crayon_1.5.2 rlang_1.0.6 #> [137] cowplot_1.1.1 KEGGREST_1.39.0 ```- [ ] I got a few errors when using the example (Seurat) data, which might be discouraging to a new user.
- [ ] Some errors appear to be because the relevant data are not available in the example object (e.g., the 'Percent mitochondria' plot in 'Quality Assurance') or the plot doesn't make sense (e.g. a 3-d version of the 'umap' or 'wnn.umap' dimensionality reductions, which I think are only 2-d). Perhaps these could be handled more gracefully?
- [ ] However, others seems to be a bigger problem. E.g., I could not get the 'Co-expression' plot to work at all with the test data. This needs to be fixed.
- [ ] Please include in the vignette a brief comparison to any other CRAN or Bioconductor-hosted packages that implement similar functionality. For example, and in particular, iSEE includes similar functionality to the 'Quality Assurance', 'Clustering', and 'Feature Expression' panels of CITEViz.
However, CITEViz's raison d'etre, 'Classifying Cell Clusters in CITE-Seq Data using the Flow Cytometry Gating Workflow', is where CITEViz distinguishes itself, I think, both in terms of purpose and implementation. There is some basic gating functionality in iSEE (see https://www.bioconductor.org/packages/devel/bioc/vignettes/iSEE/inst/doc/links.html#22_Selection_effects) and the add-on iSEEu includes some more advanced gating functionality (see
iSEEu::modeGating()), so some comparison to these would be good, but they don't seem as immediately powerful or smooth as what's available in CITEViz (although @kevinrue as developer of iSEE may well disagree with me :) ). In any case, the purpose of such a comparison is not about establishing superiority of one package over another, but to help a user navigate through the various options available to them. - [ ] I don't think spelling should appear in
DESCRIPTIONbecause it's a development-time dependency rather than something required to build, install, or use the software.
Recommended
- [ ] Consider adding a
BugReportsfield to theDESCRIPTIONlinking to the GitHub repo's issues page. - [ ] Consider adding a package-level man page.
- [ ] Please take a look at results of
covr::report()to identify under-tested areas of the package. - [ ] Probably best to include
.github, perhapsdev, and other development-only files and directories in the.Rbuildignorefile. - [ ] Minor: You refer to 'Quality Control' in vignette vs. 'Quality Assurance' in the app.
- [ ] Minor: There are some weird typos/formatting in vignette. E.g.,
- "To rename the selected cell subset after gating, double-click in the corresponding Subse- t_Name area of the data ta- type a ne w name, then press the Tab key or cl utside of the table."
- "To rename the selected cell subset after gating, double-click in the corresponding Subse- t_Name area of the data ta- type a ne w name, then press the Tab key or cl utside of the table."
bioc-issue-bot
kevinrue
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