Visualizing the spatial plots

Hi there

I did an analysis for spatial transcriptomics. After the analysis finished, I tried to visualize the spots by Spatial Plot. In following, I did spatial proximity test via Giotto package and when It finished, I tried to visualize the results as spatial plot. However, when I made a comparison between what I got from Seurat and then what I got from Giotto, it sounds on some spots, there are some discrepancies. Have you ever faced such a problem? And do you have any guess what would be the root of this issue? It should be noted that all the preprocessing steps have been done via Seurat and I transferred the data in terms of gene expression and coordinated from saved seurat obj to create a giotto obj.

This is what I got from Seurat:

And this is what I got from Giotto:

> sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS 14.5

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

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

time zone: America/Edmonton
tzcode source: internal

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

other attached packages:
[1] GiottoData_0.2.4   Seurat_5.1.0       SeuratObject_5.0.2 sp_2.1-4           Giotto_4.0.8      
[6] GiottoClass_0.3.1 

loaded via a namespace (and not attached):
  [1] RcppAnnoy_0.0.22            splines_4.3.0               later_1.3.2                
  [4] bitops_1.0-7                tibble_3.2.1                polyclip_1.10-6            
  [7] fastDummies_1.7.3           lifecycle_1.0.4             globals_0.16.3             
 [10] lattice_0.22-6              MASS_7.3-60                 backports_1.5.0            
 [13] magrittr_2.0.3              plotly_4.10.4               remotes_2.5.0              
 [16] httpuv_1.6.15               sctransform_0.4.1           spam_2.10-0                
 [19] sessioninfo_1.2.2           pkgbuild_1.4.4              spatstat.sparse_3.0-3      
 [22] reticulate_1.37.0           cowplot_1.1.3               pbapply_1.7-2              
 [25] RColorBrewer_1.1-3          abind_1.4-5                 pkgload_1.3.4              
 [28] zlibbioc_1.48.2             Rtsne_0.17                  GenomicRanges_1.54.1       
 [31] purrr_1.0.2                 BiocGenerics_0.48.1         RCurl_1.98-1.14            
 [34] GenomeInfoDbData_1.2.11     IRanges_2.36.0              S4Vectors_0.40.2           
 [37] ggrepel_0.9.5               irlba_2.3.5.1               listenv_0.9.1              
 [40] spatstat.utils_3.0-5        terra_1.7-78                goftest_1.2-3              
 [43] RSpectra_0.16-1             spatstat.random_3.2-3       fitdistrplus_1.1-11        
 [46] parallelly_1.37.1           leiden_0.4.3.1              colorRamp2_0.1.0           
 [49] codetools_0.2-20            DelayedArray_0.28.0         tidyselect_1.2.1           
 [52] farver_2.1.2                matrixStats_1.3.0           stats4_4.3.0               
 [55] spatstat.explore_3.2-7      jsonlite_1.8.8              ellipsis_0.3.2             
 [58] progressr_0.14.0            ggridges_0.5.6              survival_3.7-0             
 [61] dbscan_1.1-12               tools_4.3.0                 ica_1.0-3                  
 [64] Rcpp_1.0.12                 glue_1.7.0                  gridExtra_2.3              
 [67] SparseArray_1.2.4           MatrixGenerics_1.14.0       usethis_2.2.3              
 [70] GenomeInfoDb_1.38.8         dplyr_1.1.4                 withr_3.0.0                
 [73] fastmap_1.2.0               fansi_1.0.6                 digest_0.6.35              
 [76] R6_2.5.1                    mime_0.12                   colorspace_2.1-0           
 [79] scattermore_1.2             gtools_3.9.5                tensor_1.5                 
 [82] spatstat.data_3.0-4         utf8_1.2.4                  tidyr_1.3.1                
 [85] generics_0.1.3              data.table_1.15.4           httr_1.4.7                 
 [88] htmlwidgets_1.6.4           S4Arrays_1.2.1              uwot_0.2.2                 
 [91] pkgconfig_2.0.3             gtable_0.3.5                lmtest_0.9-40              
 [94] GiottoVisuals_0.2.3         SingleCellExperiment_1.24.0 XVector_0.42.0             
 [97] htmltools_0.5.8.1           profvis_0.3.8               dotCall64_1.1-1            
[100] scales_1.3.0                Biobase_2.62.0              GiottoUtils_0.1.8          
[103] png_0.1-8                   SpatialExperiment_1.12.0    geometry_0.4.7             
[106] rstudioapi_0.16.0           reshape2_1.4.4              rjson_0.2.21               
[109] magic_1.6-1                 checkmate_2.3.1             nlme_3.1-165               
[112] curl_5.2.1                  cachem_1.1.0                zoo_1.8-12                 
[115] stringr_1.5.1               KernSmooth_2.23-24          parallel_4.3.0             
[118] miniUI_0.1.1.1              pillar_1.9.0                grid_4.3.0                 
[121] vctrs_0.6.5                 RANN_2.6.1                  urlchecker_1.0.1           
[124] promises_1.3.0              xtable_1.8-4                cluster_2.1.6              
[127] magick_2.8.3                cli_3.6.2                   compiler_4.3.0             
[130] rlang_1.1.4                 crayon_1.5.2                future.apply_1.11.2        
[133] labeling_0.4.3              plyr_1.8.9                  fs_1.6.4                   
[136] stringi_1.8.4               viridisLite_0.4.2           deldir_2.0-4               
[139] munsell_0.5.1               lazyeval_0.2.2              devtools_2.4.5             
[142] spatstat.geom_3.2-9         Matrix_1.6-4                RcppHNSW_0.6.0             
[145] patchwork_1.2.0             future_1.33.2               ggplot2_3.5.1              
[148] shiny_1.8.1.1               SummarizedExperiment_1.32.0 ROCR_1.0-11                
[151] igraph_2.0.3                memoise_2.0.1

satijalab / seurat

Visualizing the spatial plots #9033