ImageFeaturePlot() molecules are not plotted if FOV name has "_" underscores

[alikhuseynov]

Hi there,

There is an issue with plotting molecules in ImageFeaturePlot() if FOV name has "_" underscores.
It works if dot "." is used instead.

Related issue #5819

Thanks!

[AustinHartman]

Hi, could you please post your sesssionInfo()? I thought I had fixed this before

[alikhuseynov]

Hi, thanks for reply. Yes, I think the fix was to allow for "_" in FOV names, if you have it then molecules are not plotted.
I'm using the most recent "feat/imaging" branch.

If you have a chance to take a look at subset() issue #6683 , would be very appreciated.

Thanks a lot

R version 4.2.1 (2022-06-23)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK:.. /lib/libopenblasp-r0.3.21.so

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

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

other attached packages:
[1] SeuratObject_4.1.3 Seurat_4.2.1.9000 

loaded via a namespace (and not attached):
  [1] Rtsne_0.16             colorspace_2.0-3       deldir_1.0-6          
  [4] ellipsis_0.3.2         ggridges_0.5.4         IRdisplay_1.1         
  [7] base64enc_0.1-3        spatstat.data_3.0-0    leiden_0.4.2          
 [10] listenv_0.8.0          ggrepel_0.9.2          fansi_1.0.3           
 [13] codetools_0.2-18       splines_4.2.1          polyclip_1.10-0       
 [16] IRkernel_1.3           jsonlite_1.8.0         ica_1.0-3             
 [19] cluster_2.1.4          png_0.1-7              uwot_0.1.14           
 [22] shiny_1.7.2            sctransform_0.3.5      spatstat.sparse_3.0-0 
 [25] compiler_4.2.1         httr_1.4.4             assertthat_0.2.1      
 [28] Matrix_1.5-1           fastmap_1.1.0          lazyeval_0.2.2        
 [31] cli_3.4.1              later_1.3.0            htmltools_0.5.3       
 [34] tools_4.2.1            igraph_1.3.5           gtable_0.3.1          
 [37] glue_1.6.2             RANN_2.6.1             reshape2_1.4.4        
 [40] dplyr_1.0.10           Rcpp_1.0.9             scattermore_0.8       
 [43] vctrs_0.5.0            nlme_3.1-159           spatstat.explore_3.0-5
 [46] progressr_0.11.0       lmtest_0.9-40          spatstat.random_3.0-1 
 [49] stringr_1.4.1          globals_0.16.1         mime_0.12             
 [52] miniUI_0.1.1.1         lifecycle_1.0.3        irlba_2.3.5           
 [55] goftest_1.2-3          future_1.28.0          MASS_7.3-57           
 [58] zoo_1.8-10             scales_1.2.1           promises_1.2.0.1      
 [61] spatstat.utils_3.0-1   parallel_4.2.1         RColorBrewer_1.1-3    
 [64] reticulate_1.26        pbapply_1.5-0          gridExtra_2.3         
 [67] ggplot2_3.4.0          stringi_1.7.8          repr_1.1.4            
 [70] rlang_1.0.6            pkgconfig_2.0.3        matrixStats_0.62.0    
 [73] evaluate_0.16          lattice_0.20-45        ROCR_1.0-11           
 [76] purrr_0.3.4            tensor_1.5             patchwork_1.1.2       
 [79] htmlwidgets_1.5.4      cowplot_1.1.1          tidyselect_1.1.2      
 [82] parallelly_1.32.1      RcppAnnoy_0.0.19       plyr_1.8.7            
 [85] magrittr_2.0.3         R6_2.5.1               generics_0.1.3        
 [88] pbdZMQ_0.3-7           DBI_1.1.2              pillar_1.8.1          
 [91] fitdistrplus_1.1-8     survival_3.4-0         abind_1.4-5           
 [94] sp_1.5-0               tibble_3.1.8           future.apply_1.9.0    
 [97] crayon_1.5.1           uuid_1.1-0             KernSmooth_2.23-20    
[100] utf8_1.2.2             spatstat.geom_3.0-3    plotly_4.10.0         
[103] grid_4.2.1             data.table_1.14.4      digest_0.6.29         
[106] xtable_1.8-4           tidyr_1.2.0            httpuv_1.6.5          
[109] munsell_0.5.0          viridisLite_0.4.1     

[AustinHartman]

Hi @alikhuseynov, apologies for the slow response. Now that the new Seurat spatial functionality is on CRAN, I checked this issue in Seurat 4.3.0. Seems to no longer replicate, so I'm assuming it has been fixed between then and now.