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enblacar / SCpubr

Generate high quality, publication ready visualizations for single cell transcriptomics data.
https://enblacar.github.io/SCpubr-book/
GNU General Public License v3.0
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do_AzimuthAnalysisPlot is not an exported object from 'namespace:SCpubr' #50

Closed MWRR closed 9 months ago

MWRR commented 9 months ago

Thank you for a great package. When I was trying to generate an Azimuth report out <- SCpubr::do_AzimuthAnalysisPlot(sample = harmony.Azimuth, annotation.labels = "predicted.celltype.l1", annotation.scoring = "predicted.celltype.l1.score", font.size = 18) I got this error

Error: 'do_AzimuthAnalysisPlot' is not an exported object from 'namespace:SCpubr'

sessionInfo()

R version 4.3.2 (2023-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale:
[1] LC_COLLATE=English_Australia.utf8  LC_CTYPE=English_Australia.utf8    LC_MONETARY=English_Australia.utf8
[4] LC_NUMERIC=C                       LC_TIME=English_Australia.utf8    

time zone: Australia/Sydney
tzcode source: internal

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

other attached packages:
[1] SCpubr_2.0.2       dplyr_1.1.4        pheatmap_1.0.12    ggplot2_3.4.4      patchwork_1.2.0    SeuratObject_4.1.4
[7] Seurat_4.4.0      

loaded via a namespace (and not attached):
  [1] RcppAnnoy_0.0.21              splines_4.3.2                 later_1.3.2                  
  [4] bitops_1.0-7                  filelock_1.0.3                tibble_3.2.1                 
  [7] polyclip_1.10-6               lifecycle_1.0.4               globals_0.16.2               
 [10] lattice_0.22-5                MASS_7.3-60                   magrittr_2.0.3               
 [13] plotly_4.10.3                 rmarkdown_2.25                yaml_2.3.8                   
 [16] httpuv_1.6.13                 sctransform_0.4.1             spam_2.10-0                  
 [19] sp_2.1-2                      spatstat.sparse_3.0-3         reticulate_1.34.0            
 [22] cowplot_1.1.2                 pbapply_1.7-2                 DBI_1.2.0                    
 [25] RColorBrewer_1.1-3            abind_1.4-5                   zlibbioc_1.48.0              
 [28] Rtsne_0.17                    GenomicRanges_1.54.1          purrr_1.0.2                  
 [31] BiocGenerics_0.48.1           RCurl_1.98-1.14               rappdirs_0.3.3               
 [34] GenomeInfoDbData_1.2.11       IRanges_2.36.0                S4Vectors_0.40.2             
 [37] ggrepel_0.9.4                 irlba_2.3.5.1                 listenv_0.9.0                
 [40] spatstat.utils_3.0-4          goftest_1.2-3                 spatstat.random_3.2-2        
 [43] fitdistrplus_1.1-11           parallelly_1.36.0             DelayedMatrixStats_1.24.0    
 [46] leiden_0.4.3.1                codetools_0.2-19              DelayedArray_0.28.0          
 [49] tidyselect_1.2.0              matrixStats_1.2.0             stats4_4.3.2                 
 [52] BiocFileCache_2.10.1          spatstat.explore_3.2-5        jsonlite_1.8.8               
 [55] ellipsis_0.3.2                progressr_0.14.0              ggridges_0.5.5               
 [58] survival_3.5-7                tools_4.3.2                   ica_1.0-3                    
 [61] Rcpp_1.0.12                   glue_1.7.0                    gridExtra_2.3                
 [64] SparseArray_1.2.3             xfun_0.41                     MatrixGenerics_1.14.0        
 [67] GenomeInfoDb_1.38.5           withr_2.5.2                   BiocManager_1.30.22          
 [70] fastmap_1.1.1                 fansi_1.0.6                   digest_0.6.34                
 [73] R6_2.5.1                      mime_0.12                     colorspace_2.1-0             
 [76] scattermore_1.2               tensor_1.5                    spatstat.data_3.0-3          
 [79] RSQLite_2.3.4                 celldex_1.12.0                utf8_1.2.4                   
 [82] tidyr_1.3.0                   generics_0.1.3                data.table_1.14.10           
 [85] httr_1.4.7                    htmlwidgets_1.6.4             S4Arrays_1.2.0               
 [88] uwot_0.1.16                   pkgconfig_2.0.3               gtable_0.3.4                 
 [91] blob_1.2.4                    lmtest_0.9-40                 XVector_0.42.0               
 [94] htmltools_0.5.7               dotCall64_1.1-1               scales_1.3.0                 
 [97] Biobase_2.62.0                png_0.1-8                     knitr_1.45                   
[100] rstudioapi_0.15.0             reshape2_1.4.4                nlme_3.1-164                 
[103] curl_5.2.0                    cachem_1.0.8                  zoo_1.8-12                   
[106] stringr_1.5.1                 BiocVersion_3.18.1            KernSmooth_2.23-22           
[109] parallel_4.3.2                miniUI_0.1.1.1                AnnotationDbi_1.64.1         
[112] pillar_1.9.0                  grid_4.3.2                    vctrs_0.6.5                  
[115] RANN_2.6.1                    promises_1.2.1                dbplyr_2.4.0                 
[118] xtable_1.8-4                  cluster_2.1.6                 evaluate_0.23                
[121] cli_3.6.2                     compiler_4.3.2                rlang_1.1.3                  
[124] crayon_1.5.2                  future.apply_1.11.1           plyr_1.8.9                   
[127] stringi_1.8.3                 viridisLite_0.4.2             deldir_2.0-2                 
[130] munsell_0.5.0                 Biostrings_2.70.1             lazyeval_0.2.2               
[133] spatstat.geom_3.2-7           Matrix_1.6-4                  ExperimentHub_2.10.0         
[136] sparseMatrixStats_1.14.0      bit64_4.0.5                   future_1.33.1                
[139] KEGGREST_1.42.0               shiny_1.8.0                   SummarizedExperiment_1.32.0  
[142] interactiveDisplayBase_1.40.0 AnnotationHub_3.10.0          ROCR_1.0-11                  
[145] igraph_1.6.0                  memoise_2.0.1                 bit_4.0.5
enblacar commented 9 months ago

Hi @MWRR,

Thanks for using my package!

This function was removed when updating to SCpubr v2.0.0. You can find more info here and here.

Hope that helps! Enrique

MWRR commented 9 months ago

Hi @MWRR,

Thanks for using my package!

This function was removed when updating to SCpubr v2.0.0. You can find more info here and here.

Hope that helps! Enrique

Thanks for quick reply. Has an updated vignette been added to generate the same analysis by a combination of the available functions?

enblacar commented 9 months ago

Hi @MWRR,

Unfortunately, I was not able to finish the new documentation as I would have liked by the release of v2. This is not likely going to happen before I finish my PhD in the following months.

Here is a link to the code that generated the report: https://github.com/enblacar/SCpubr/blob/9bdb16c62a2a239168c8f0b35fa6c76c0031c0b3/R/do_AzimuthAnalysisPlot.R#L186

However, if it is just a quick report what you want to generate, I'd advise downgrading to v1.1.2 to do it, and then update back to v2.0.2.

Sorry for the inconveniences! Enrique