object 'NicheData10x' not found

[ogola89]

Hi there,

While going through the vignette, I am encountering a problem as to the NicheData10x object. The object seems to not be found. I am running rnamagnet 0.1.0 and seurat 3.2.0.

I have been unable to find this object in any of the subfolders of the rnamagnet nor does data (NicheData10x) work.

Do you know how I can solve this? Is there a downloadable NicheData10x file that can be loaded into R and used in the same way?

This happened when running the qplot function. See below with error and sessionInfo.

> qplot(x = Embeddings(NicheData10x,reduction="tsne")[,1], y = Embeddings(NicheData10x,reduction="tsne")[,2], color =Idents(NicheData10x)) + scale_color_manual(values = NicheDataColors) + theme_bw() + theme(panel.grid = element_blank(), axis.text = element_blank(), axis.title = element_blank())
Error in Embeddings(NicheData10x, reduction = "tsne") : 
  object 'NicheData10x' not found

> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19041)

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                            LC_TIME=English_United Kingdom.1252    

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

other attached packages:
 [1] Seurat_3.2.0           RNAMagnet_0.1.0        rWikiPathways_1.8.4    clusterProfiler_3.16.1 magrittr_1.5          
 [6] msigdbr_7.1.1          org.Hs.eg.db_3.11.4    AnnotationDbi_1.50.3   IRanges_2.22.2         S4Vectors_0.26.1      
[11] forcats_0.5.0          stringr_1.4.0          dplyr_1.0.2            purrr_0.3.4            readr_1.3.1           
[16] tidyr_1.1.2            tibble_3.0.3           ggplot2_3.3.2          tidyverse_1.3.0        DOSE_3.14.0           
[21] Biobase_2.48.0         BiocGenerics_0.34.0   

loaded via a namespace (and not attached):
  [1] reticulate_1.16       tidyselect_1.1.0      htmlwidgets_1.5.1     RSQLite_2.2.0         grid_4.0.2           
  [6] BiocParallel_1.22.0   Rtsne_0.15            lpSolve_5.6.15        devtools_2.3.1        scatterpie_0.1.4     
 [11] munsell_0.5.0         codetools_0.2-16      ica_1.0-2             preprocessCore_1.50.0 future_1.18.0        
 [16] miniUI_0.1.1.1        withr_2.2.0           colorspace_1.4-1      GOSemSim_2.14.1       limSolve_1.5.6       
 [21] knitr_1.29            rstudioapi_0.11       ROCR_1.0-11           tensor_1.5            listenv_0.8.0        
 [26] labeling_0.3          urltools_1.7.3        polyclip_1.10-0       bit64_4.0.2           farver_2.0.3         
 [31] rprojroot_1.3-2       downloader_0.4        vctrs_0.3.3           generics_0.0.2        xfun_0.15            
 [36] R6_2.4.1              graphlayouts_0.7.0    rsvd_1.0.3            locfit_1.5-9.4        spatstat.utils_1.17-0
 [41] bitops_1.0-6          fgsea_1.14.0          gridGraphics_0.5-0    assertthat_0.2.1      promises_1.1.1       
 [46] scales_1.1.1          ggraph_2.0.3          enrichplot_1.8.1      gtable_0.3.0          globals_0.12.5       
 [51] sva_3.36.0            processx_3.4.3        goftest_1.2-2         tidygraph_1.2.0       rlang_0.4.7          
 [56] genefilter_1.70.0     splines_4.0.2         lazyeval_0.2.2        EPIC_1.1.5            broom_0.7.0          
 [61] europepmc_0.4         abind_1.4-5           BiocManager_1.30.10   yaml_2.2.1            reshape2_1.4.4       
 [66] modelr_0.1.8          backports_1.1.7       httpuv_1.5.4          qvalue_2.20.0         usethis_1.6.1        
 [71] tools_4.0.2           ggplotify_0.0.5       ellipsis_0.3.1        RColorBrewer_1.1-2    sessioninfo_1.1.1    
 [76] ggridges_0.5.2        testit_0.11           Rcpp_1.0.5            plyr_1.8.6            progress_1.2.2       
 [81] RCurl_1.98-1.2        ps_1.3.4              prettyunits_1.1.1     deldir_0.1-28         rpart_4.1-15         
 [86] pbapply_1.4-3         viridis_0.5.1         cowplot_1.0.0         zoo_1.8-8             haven_2.3.1          
 [91] ggrepel_0.8.2         cluster_2.1.0         fs_1.5.0              tinytex_0.25          data.table_1.13.0    
 [96] DO.db_2.9             triebeard_0.3.0       lmtest_0.9-37         reprex_0.3.0          RANN_2.6.1           
[101] fitdistrplus_1.1-1    matrixStats_0.56.0    pkgload_1.1.0         hms_0.5.3             patchwork_1.0.1      
[106] mime_0.9              evaluate_0.14         xtable_1.8-4          XML_3.99-0.5          readxl_1.3.1         
[111] gridExtra_2.3         testthat_2.3.2        compiler_4.0.2        KernSmooth_2.23-17    crayon_1.3.4         
[116] htmltools_0.5.0       mgcv_1.8-31           later_1.1.0.1         snow_0.4-3            lubridate_1.7.9      
[121] DBI_1.1.0             tweenr_1.0.1          dbplyr_1.4.4          MASS_7.3-51.6         rappdirs_0.3.1       
[126] data.tree_1.0.0       Matrix_1.2-18         cli_2.0.2             quadprog_1.5-8        igraph_1.2.5         
[131] pkgconfig_2.0.3       rvcheck_0.1.8         plotly_4.9.2.1        xml2_1.3.2            annotate_1.66.0      
[136] rvest_0.3.6           callr_3.4.3           digest_0.6.25         sctransform_0.2.1     RcppAnnoy_0.0.16     
[141] spatstat.data_1.4-3   rmarkdown_2.3         cellranger_1.1.0      leiden_0.3.3          fastmatch_1.1-0      
[146] uwot_0.1.8            edgeR_3.30.3          curl_4.3              shiny_1.5.0           rjson_0.2.20         
[151] lifecycle_0.2.0       nlme_3.1-148          jsonlite_1.7.0        desc_1.2.0            viridisLite_0.3.0    
[156] limma_3.44.3          fansi_0.4.1           pillar_1.4.6          lattice_0.20-41       pkgbuild_1.1.0       
[161] fastmap_1.0.1         httr_1.4.2            survival_3.1-12       GO.db_3.11.4          remotes_2.2.0        
[166] glue_1.4.2            spatstat_1.64-1       png_0.1-7             bit_4.0.4             immunedeconv_2.0.3   
[171] ggforce_0.3.2         stringi_1.4.6         blob_1.2.1            memoise_1.1.0         irlba_2.3.3          
[176] future.apply_1.6.0    ape_5.4-1    

[alecorr]

Hi,

If you are having issues finding the NicheData10x.rda in the rna magnet zipped folder (https://www.dropbox.com/s/wbnqaebqi74j5ic/RNAMagnetDataBundle.zip), the data is also available to download directly from the paper itself (https://www.nature.com/articles/s41556-019-0439-6#Sec28). Just click the link labelled 'Supplementary Data' within the supplementary information section to download and then unzip to access the 4 rda files (NicheData10x.rda, NicheDataLCM.rda, NicheMarkers10x.rda, NicheMetaDataLCM.rda) and a readme explanation of the data. From your post, it sounds like the seurat object stored in NicheData10x.rda is the one you're after.

Hope this helps! Alex (not part of the Velten lab)

[velten-lab]

Thanks Alex!

[ogola89]

Thanks for this, it's great

[alecorr]

No worries!

Also thanks @velten-lab for providing the finalised seurat object with their publication - I think it's a practice that more labs should follow