Spatial Proteomics of a Human Brain Tumour

Code to reproduce spatial proteomic analysis from Davis et al. "Deep topographic proteomics of a human brain tumour"

The analysis is included as an Rmarkdown html file (SpatialAnalysis.html), the corresponding SpatialAnalysis.Rmd file, and the input data.

Installation and running:
1. Download this directory
2. Open SpatialAnalysis.Rmd in RStudio
3. Modify the working directory to reflect the location of the SpatialAnalysis.Rmd file (line 20). Ensure 'Data' folder is present too.
4. If recalculating Moran's index and not using provided precalculated values, comment/uncomment lines as guided in the file (line 241)
5. Run all (Ctrl+Alt+R)

Runtime is less than 10 minutes on an i7 laptop with 16 GB RAM and an SSD using 4 logical cores for calculation of Moran's Index

Expected output:
In-line graphs of proteomic maps and cluster map

Tested on R4.3.1 on Windows 10 (details below)
> sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.utf8  LC_CTYPE=English_United Kingdom.utf8   
[3] LC_MONETARY=English_United Kingdom.utf8 LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.utf8    

time zone: Europe/London
tzcode source: internal

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

other attached packages:
[1] reshape2_1.4.4        knitr_1.44            ggplot2_3.4.3         RColorBrewer_1.1-3    dynamicTreeCut_1.63-1
[6] data.table_1.14.8     plot.matrix_1.6.2     viridis_0.6.4         viridisLite_0.4.2     scales_1.2.1         
[11] doParallel_1.0.17     iterators_1.0.14      foreach_1.5.2         raster_3.6-23         sp_2.0-0             
[16] spdep_1.2-8           sf_1.0-14             spData_2.3.0          dplyr_1.1.3           pacman_0.5.1         

loaded via a namespace (and not attached):
[1] s2_1.1.4           utf8_1.2.3         generics_0.1.3     class_7.3-22       KernSmooth_2.23-21 stringi_1.7.12    
 [7] lattice_0.21-8     magrittr_2.0.3     grid_4.3.1         plyr_1.8.8         e1071_1.7-13       DBI_1.1.3         
[13] gridExtra_2.3      fansi_1.0.4        codetools_0.2-19   cli_3.6.1          rlang_1.1.1        units_0.8-3       
[19] munsell_0.5.0      withr_2.5.0        tools_4.3.1        deldir_1.0-9       colorspace_2.1-0   boot_1.3-28.1     
[25] vctrs_0.6.3        R6_2.5.1           proxy_0.4-27       lifecycle_1.0.3    classInt_0.4-10    stringr_1.5.0     
[31] pkgconfig_2.0.3    terra_1.7-46       pillar_1.9.0       gtable_0.3.4       glue_1.6.2         Rcpp_1.0.11       
[37] xfun_0.40          tibble_3.2.1       tidyselect_1.2.0   farver_2.1.1       labeling_0.4.3     wk_0.8.0          
[43] compiler_4.3.1