SpatialPlot problems

[wakelin-g]

Hi all,

I am trying to output something generated using the SpatialPlot function as an EPS file, however for some reason it removes all of my data points.

Here is the output in R:

However, when I export this as an EPS and open it in illustrator I only get the following:

I am wondering if anyone has any ideas as to why the rest of my data points aren't showing up. The problem only seems to occur with the EPS file format, as I can export it as a PNG without any issues.

Any advice would be of help,

Griffen

R version 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)

Matrix products: default

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

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

other attached packages:
 [1] sloop_1.0.1         scico_1.2.0.9000    devtools_2.4.2      usethis_2.0.1       viridis_0.6.1       viridisLite_0.4.0  
 [7] nnls_1.4            edgeR_3.34.0        limma_3.48.1        NMF_0.23.0          cluster_2.1.2       rngtools_1.5       
[13] pkgmaker_0.32.2     registry_0.5-1      RColorBrewer_1.1-2  igraph_1.2.6        SPOTlight_0.1.7     gt_0.3.0           
[19] data.table_1.14.0   reticulate_1.20     forcats_0.5.1       stringr_1.4.0       purrr_0.3.4         readr_1.4.0        
[25] tidyr_1.1.3         tibble_3.1.2        ggplot2_3.3.5       tidyverse_1.3.1     Matrix_1.3-3        dplyr_1.0.7        
[31] SeuratObject_4.0.2  Seurat_4.0.3        Biobase_2.52.0      BiocGenerics_0.38.0

loaded via a namespace (and not attached):
  [1] utf8_1.2.1            tidyselect_1.1.1      htmlwidgets_1.5.3     grid_4.1.0            Rtsne_0.15           
  [6] munsell_0.5.0         codetools_0.2-18      ica_1.0-2             DT_0.18               future_1.21.0        
 [11] miniUI_0.1.1.1        withr_2.4.2           colorspace_2.0-2      rstudioapi_0.13       ROCR_1.0-11          
 [16] tensor_1.5            listenv_0.8.0         labeling_0.4.2        polyclip_1.10-0       bit64_4.0.5          
 [21] farver_2.1.0          rprojroot_2.0.2       parallelly_1.27.0     vctrs_0.3.8           generics_0.1.0       
 [26] xfun_0.24             R6_2.5.1              doParallel_1.0.16     locfit_1.5-9.4        hdf5r_1.3.3          
 [31] spatstat.utils_2.2-0  cachem_1.0.5          assertthat_0.2.1      promises_1.2.0.1      scales_1.1.1         
 [36] gtable_0.3.0          globals_0.14.0        processx_3.5.2        goftest_1.2-2         rlang_0.4.11         
 [41] splines_4.1.0         lazyeval_0.2.2        spatstat.geom_2.2-2   broom_0.7.9           checkmate_2.0.0      
 [46] yaml_2.2.1            reshape2_1.4.4        abind_1.4-5           modelr_0.1.8          crosstalk_1.1.1      
 [51] backports_1.2.1       httpuv_1.6.1          tools_4.1.0           gridBase_0.4-7        ellipsis_0.3.2       
 [56] spatstat.core_2.3-0   jquerylib_0.1.4       sessioninfo_1.1.1     ggridges_0.5.3        Rcpp_1.0.7           
 [61] plyr_1.8.6            ps_1.6.0              prettyunits_1.1.1     rpart_4.1-15          deldir_0.2-10        
 [66] pbapply_1.4-3         cowplot_1.1.1         zoo_1.8-9             haven_2.4.1           ggrepel_0.9.1        
 [71] fs_1.5.0              tinytex_0.32          magrittr_2.0.1        RSpectra_0.16-0       scattermore_0.7      
 [76] lmtest_0.9-38         reprex_2.0.0          RANN_2.6.1            fitdistrplus_1.1-5    matrixStats_0.59.0   
 [81] pkgload_1.2.1         hms_1.1.0             patchwork_1.1.1       mime_0.11             xtable_1.8-4         
 [86] readxl_1.3.1          gridExtra_2.3         testthat_3.0.4        compiler_4.1.0        KernSmooth_2.23-20   
 [91] crayon_1.4.1          htmltools_0.5.1.1     mgcv_1.8-35           later_1.2.0           lubridate_1.7.10     
 [96] DBI_1.1.1             dbplyr_2.1.1          MASS_7.3-54           cli_3.0.0             pkgconfig_2.0.3      
[101] plotly_4.9.4.1        spatstat.sparse_2.0-0 xml2_1.3.2            foreach_1.5.1         bslib_0.2.5.1        
[106] rvest_1.0.1           callr_3.7.0           digest_0.6.27         sctransform_0.3.2     RcppAnnoy_0.0.18     
[111] spatstat.data_2.1-0   cellranger_1.1.0      leiden_0.3.9          uwot_0.1.10           curl_4.3.2           
[116] shiny_1.6.0           lifecycle_1.0.0       nlme_3.1-152          jsonlite_1.7.2        desc_1.3.0           
[121] fansi_0.5.0           pillar_1.6.2          lattice_0.20-44       fastmap_1.1.0         httr_1.4.2           
[126] pkgbuild_1.2.0        survival_3.2-11       glue_1.4.2            remotes_2.4.0         png_0.1-7            
[131] iterators_1.0.13      bit_4.0.4             stringi_1.6.2         sass_0.4.0            memoise_2.0.0        
[136] irlba_2.3.3           future.apply_1.7.0

[wakelin-g]

Beginner mistake I guess--EPS doesn't support transparency. The workaround was to export them as SVG instead.