'Crop' Function Failed on Vizgen Data

[tangboyun]

I am following the tutorial on Vizgen data analysis.

vizgen.obj <- LoadVizgen(data.dir = '/path/to/input_dir', fov = 'fov',verbose=TRUE)
vizgen.obj <- SCTransform(vizgen.obj, assay = 'Vizgen', clip.range = c(-10, 10), )
vizgen.obj <- RunPCA(vizgen.obj, npcs = 30, features = rownames(vizgen.obj))
vizgen.obj <- RunUMAP(vizgen.obj, dims = 1:30)
vizgen.obj <- FindNeighbors(vizgen.obj, reduction = 'pca', dims = 1:30)
vizgen.obj <- FindClusters(vizgen.obj, resolution = 0.3)

When I tried to create a Crop, I got the following error:

vizgen.crop <- Crop(vizgen.obj[['fov']],x=c(1250,3750),y=c(8000,9000),coords='plot')
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'y' in selecting a method for function 'Overlay': cannot derive coordinates from non-numeric matrix
Calls: Crop ... stopifnot -> Polygon -> coordinates -> coordinates -> .local

My ImageDimPlot looks like this:

I've tried to swap the x and y coordinates, and tried other ranges like x=c(8000,9000),y=c(8000,9000) or x=c(1000,2000),y=c(1000,2000). But I still got the same error.

I've installed the latest patch in #7190 and my sessionInfo() is:

R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.2 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

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

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

other attached packages:
 [1] spatstat_3.0-6          spatstat.linnet_3.1-1   spatstat.model_3.2-4   
 [4] rpart_4.1.16            spatstat.explore_3.2-1  nlme_3.1-155           
 [7] spatstat.random_3.1-5   spatstat.geom_3.2-4     spatstat.data_3.0-1    
[10] progressr_0.13.0        BiocParallel_1.34.2     magrittr_2.0.3         
[13] dplyr_1.1.2             SeuratObject_4.9.9.9091 Seurat_4.3.0.9002      

loaded via a namespace (and not attached):
 [1] spatstat.sparse_3.0-2 matrixStats_1.0.0     RcppAnnoy_0.0.21     
 [4] RColorBrewer_1.1-3    httr_1.4.6            sctransform_0.3.5    
 [7] tools_4.1.2           utf8_1.2.3            R6_2.5.1             
[10] irlba_2.3.5.1         KernSmooth_2.23-20    mgcv_1.8-39          
[13] uwot_0.1.16           lazyeval_0.2.2        colorspace_2.1-0     
[16] sp_2.0-0              tidyselect_1.2.0      gridExtra_2.3        
[19] compiler_4.1.2        cli_3.6.1             plotly_4.10.2        
[22] scales_1.2.1          lmtest_0.9-40         ggridges_0.5.4       
[25] pbapply_1.7-2         goftest_1.2-3         stringr_1.5.0        
[28] digest_0.6.33         spatstat.utils_3.0-3  pkgconfig_2.0.3      
[31] htmltools_0.5.5       parallelly_1.36.0     fastmap_1.1.1        
[34] htmlwidgets_1.6.2     rlang_1.1.1           shiny_1.7.4.1        
[37] generics_0.1.3        zoo_1.8-12            jsonlite_1.8.7       
[40] ica_1.0-3             dotCall64_1.0-2       patchwork_1.1.2      
[43] Matrix_1.6-0          Rcpp_1.0.11           munsell_0.5.0        
[46] fansi_1.0.4           abind_1.4-5           reticulate_1.30      
[49] lifecycle_1.0.3       stringi_1.7.12        MASS_7.3-55          
[52] Rtsne_0.16            plyr_1.8.8            grid_4.1.2           
[55] parallel_4.1.2        listenv_0.9.0         promises_1.2.0.1     
[58] ggrepel_0.9.3         deldir_1.0-9          miniUI_0.1.1.1       
[61] lattice_0.20-45       cowplot_1.1.1         splines_4.1.2        
[64] tensor_1.5            pillar_1.9.0          igraph_1.5.0.1       
[67] future.apply_1.11.0   reshape2_1.4.4        codetools_0.2-18     
[70] leiden_0.4.3          glue_1.6.2            data.table_1.14.8    
[73] png_0.1-8             vctrs_0.6.3           spam_2.9-1           
[76] httpuv_1.6.11         polyclip_1.10-4       gtable_0.3.3         
[79] RANN_2.6.1            purrr_1.0.1           tidyr_1.3.0          
[82] scattermore_1.2       future_1.33.0         ggplot2_3.4.2        
[85] mime_0.12             xtable_1.8-4          later_1.3.1          
[88] survival_3.2-13       viridisLite_0.4.2     tibble_3.2.1         
[91] cluster_2.1.2         globals_0.16.2        fitdistrplus_1.1-11  
[94] ellipsis_0.3.2        ROCR_1.0-11

[alikhuseynov]

were those red star shapes added on purpose?
Note that Crop function is from SeuratObject package.
Does it work if you use coords = "tissue" with x=c(8000, 9000), y=c(8000, 9000) ?

[tangboyun]

My fault...
I forgot to set the options options(Seurat.object.assay.version = "v5"). Setting the options will cause another error: GetAssay(vizgen.obj,assay='Vizgen') will not work. I'll close this issue and open a new issue.