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satijalab / azimuth

A Shiny web app for mapping datasets using Seurat v4
https://satijalab.org/azimuth
GNU General Public License v3.0
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Error in match arguments #111

Closed susheelbhanu closed 2 years ago

susheelbhanu commented 2 years ago

Hi,

I'm trying to annotate a seurate object and getting the following error. 

azimuth_gm.combined <- RunAzimuth(gm.combined, reference = "mousecortexref")
Error in match.arg(arg = tolower(x = type), choices = c("raw", "default",  : 
  'arg' should be one of “raw”, “default”, “NA”, “NA”

Could you please let me know how to fix this?

Thank you!

AustinHartman commented 2 years ago

Could you please post your sessionInfo()?

susheelbhanu commented 2 years ago

Here you go... Sorry it's bloated, 'cos I'm working on a few things simultaneously ;)

sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: OS X  12.4

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] biomaRt_2.46.3                  scmap_1.12.0                   
 [3] CHETAH_1.6.0                    SingleCellExperiment_1.12.0    
 [5] SummarizedExperiment_1.20.0     Biobase_2.50.0                 
 [7] GenomicRanges_1.42.0            GenomeInfoDb_1.26.7            
 [9] IRanges_2.24.1                  S4Vectors_0.28.1               
[11] BiocGenerics_0.36.0             MatrixGenerics_1.2.0           
[13] matrixStats_0.57.0              mousecortexref.SeuratData_1.0.0
[15] Azimuth_0.4.5                   shinyBS_0.61.1                 
[17] metap_1.7                       ifnb.SeuratData_3.1.0          
[19] SeuratData_0.2.1                fgsea_1.16.0                   
[21] msigdbr_7.5.1                   presto_1.0.0                   
[23] data.table_1.13.6               cowplot_1.1.1                  
[25] babelgene_22.3                  patchwork_1.1.1                
[27] sp_1.4-5                        SeuratObject_4.1.0             
[29] Seurat_4.1.1                    Rcpp_1.0.7                     
[31] reshape_0.8.8                   rstatix_0.7.0                  
[33] pairwiseAdonis_0.4              cluster_2.1.0                  
[35] vegan_2.5-7                     lattice_0.20-41                
[37] permute_0.9-5                   ggpubr_0.4.0                   
[39] RColorBrewer_1.1-2              knitr_1.39                     
[41] microbiome_1.12.0               phyloseq_1.34.0                
[43] ggrepel_0.9.1                   keyplayer_1.0.3                
[45] reshape2_1.4.4                  influenceR_0.1.0.1             
[47] ggsci_2.9                       Matrix_1.4-0                   
[49] SpiecEasi_1.1.0                 janitor_2.1.0                  
[51] forcats_0.5.1                   stringr_1.4.0                  
[53] dplyr_1.0.5                     purrr_0.3.4                    
[55] readr_1.4.0                     tidyr_1.1.3                    
[57] tibble_3.1.0                    ggplot2_3.3.3                  
[59] tidyverse_1.3.1                 igraph_1.2.6                   

loaded via a namespace (and not attached):
  [1] ica_1.0-2              class_7.3-17           ps_1.5.0              
  [4] foreach_1.5.1          lmtest_0.9-39          rprojroot_2.0.2       
  [7] glmnet_4.0-2           crayon_1.4.1           spatstat.core_2.3-2   
 [10] rbibutils_2.2.7        MASS_7.3-53            rhdf5filters_1.2.0    
 [13] nlme_3.1-151           backports_1.2.1        reprex_2.0.0          
 [16] huge_1.3.4.1           rlang_0.4.10           XVector_0.30.0        
 [19] ROCR_1.0-11            readxl_1.3.1           irlba_2.3.5           
 [22] callr_3.6.0            limma_3.46.0           BiocParallel_1.24.1   
 [25] bit64_4.0.5            glue_1.4.2             pheatmap_1.0.12       
 [28] sctransform_0.3.3      processx_3.5.1         AnnotationDbi_1.52.0  
 [31] spatstat.sparse_2.1-0  SeuratDisk_0.0.0.9020  shinydashboard_0.7.2  
 [34] spatstat.geom_2.4-0    VGAM_1.1-5             haven_2.3.1           
 [37] tidyselect_1.1.0       usethis_2.0.0          rio_0.5.16            
 [40] fitdistrplus_1.1-6     XML_3.99-0.5           zoo_1.8-8             
 [43] xtable_1.8-4           magrittr_2.0.1         Rdpack_2.1.3          
 [46] cli_2.4.0              zlibbioc_1.36.0        pulsar_0.3.7          
 [49] sn_2.0.1               rstudioapi_0.13        miniUI_0.1.1.1        
 [52] rpart_4.1-15           fastmatch_1.1-3        mathjaxr_1.4-0        
 [55] shiny_1.6.0            xfun_0.30              askpass_1.1           
 [58] pkgbuild_1.2.0         multtest_2.46.0        caTools_1.18.0        
 [61] biomformat_1.18.0      ape_5.4-1              listenv_0.8.0         
 [64] dendextend_1.14.0      Biostrings_2.58.0      png_0.1-7             
 [67] future_1.23.0          withr_2.3.0            bitops_1.0-6          
 [70] plyr_1.8.6             cellranger_1.1.0       e1071_1.7-7           
 [73] pillar_1.6.0           gplots_3.1.1           multcomp_1.4-15       
 [76] fs_1.5.0               hdf5r_1.3.5            googleVis_0.7.0       
 [79] vctrs_0.3.6            ellipsis_0.3.1         generics_0.1.0        
 [82] devtools_2.3.2         tools_4.0.2            foreign_0.8-81        
 [85] munsell_0.5.0          proxy_0.4-25           DelayedArray_0.16.0   
 [88] fastmap_1.1.0          compiler_4.0.2         pkgload_1.1.0         
 [91] abind_1.4-5            httpuv_1.5.5           sessioninfo_1.1.1     
 [94] plotly_4.9.3           rgeos_0.5-9            GenomeInfoDbData_1.2.4
 [97] gridExtra_2.3          deldir_1.0-6           mutoss_0.1-12         
[100] utf8_1.1.4             later_1.1.0.1          BiocFileCache_1.14.0  
[103] jsonlite_1.7.2         scales_1.1.1           pbapply_1.4-3         
[106] carData_3.0-4          lazyeval_0.2.2         promises_1.1.1        
[109] car_3.0-10             goftest_1.2-3          spatstat.utils_2.3-0  
[112] reticulate_1.22        openxlsx_4.2.3.9000    sandwich_3.0-0        
[115] Rtsne_0.15             uwot_0.1.11            survival_3.2-7        
[118] numDeriv_2016.8-1.1    plotrix_3.8-2          htmltools_0.5.1.1     
[121] memoise_1.1.0          viridisLite_0.3.0      digest_0.6.27         
[124] assertthat_0.2.1       mime_0.9               rappdirs_0.3.1        
[127] RSQLite_2.2.1          future.apply_1.8.1     remotes_2.2.0         
[130] blob_1.2.1             splines_4.0.2          labeling_0.4.2        
[133] Rhdf5lib_1.12.0        googledrive_1.0.1      RCurl_1.98-1.2        
[136] broom_0.7.6            hms_1.0.0              modelr_0.1.8          
[139] rhdf5_2.34.0           colorspace_2.0-0       BiocManager_1.30.10   
[142] mnormt_2.0.2           shape_1.4.5            tmvnsim_1.0-2         
[145] RANN_2.6.1             mvtnorm_1.1-1          fansi_0.4.1           
[148] parallelly_1.30.0      R6_2.5.0               grid_4.0.2            
[151] ggridges_0.5.2         lifecycle_1.0.0        zip_2.1.1             
[154] bioDist_1.62.0         TFisher_0.2.0          curl_4.3              
[157] ggsignif_0.6.3         googlesheets4_0.3.0    leiden_0.3.9          
[160] testthat_3.0.1         snakecase_0.11.0       desc_1.2.0            
[163] RcppAnnoy_0.0.19       TH.data_1.0-10         iterators_1.0.13      
[166] htmlwidgets_1.5.3      polyclip_1.10-0        rvest_1.0.0           
[169] mgcv_1.8-33            globals_0.14.0         openssl_1.4.3         
[172] progressr_0.10.0       codetools_0.2-18       lubridate_1.7.10      
[175] randomForest_4.6-14    gtools_3.8.2           prettyunits_1.1.1     
[178] dbplyr_2.1.1           gtable_0.3.0           DBI_1.1.0             
[181] tensor_1.5             httr_1.4.2             KernSmooth_2.23-18    
[184] stringi_1.5.3          progress_1.2.2         farver_2.0.3          
[187] viridis_0.5.1          DT_0.16                xml2_1.3.2            
[190] shinyjs_2.1.0          ade4_1.7-16            scattermore_0.7       
[193] bit_4.0.4              spatstat.data_2.1-2    pkgconfig_2.0.3       
[196] gargle_1.1.0           corrplot_0.84
AustinHartman commented 2 years ago

Try installing v0.2.2 of SeuratData and let me know if that fixes the issue. I'll make sure to set the minimum version required by Azimuth in future updates

susheelbhanu commented 2 years ago

Okay, I have this: SeuratData_0.2.2, but still getting the same error.

AustinHartman commented 2 years ago

Thanks for trying that - I'm unable to replicate this error myself so I suspect it may have something to do with the Seurat object passed to RunAzimuth. Any chance you could email me a small Seurat object I can reproduce the error with in order to debug? My email is ahartman@nygenome.org

susheelbhanu commented 2 years ago

Thank you. Sent you the data via email.

AustinHartman commented 2 years ago

Solved over email by upgrading SeuratData to v0.2.2 and restarting RStudio