Biological contribution of phenotype data on cytokine expression in each cell-type from DLPFC region.

Cell types

Excitatory Neurons

Inhibitory Neurons

Microglia

Oligodendrocytes

Astrocytes

Oligodendrocyte progenitor cells

Endothelial cells

### Getting variance results

# function
extract_vp <- function(res_vp, cell){
  df <- res_vp %>% 
    as.data.frame() %>% 
    mutate(cell_type = cell, gene_name = rownames(res_vp)) %>%  
    select(gene_name, cell_type, everything())
  
  rownames(df) <- NULL  # Remove os nomes das linhas
  
  return(df)
}

# extract vp 
variance_ext <- extract_vp(result_ext[["vp"]], "ext")
variance_inh <- extract_vp(result_inh[["vp"]], "inh")
variance_mic <- extract_vp(result_mic[["vp"]], "mic")
variance_ast <- extract_vp(result_ast[["vp"]], "ast")
variance_oli <- extract_vp(result_oli[["vp"]], "oli")
variance_opc <- extract_vp(result_opc[["vp"]], "opc")
variance_end <- extract_vp(result_end[["vp"]], "end")

final_matrix_variance <- variance_ext %>% 
  bind_rows(variance_inh, variance_mic, variance_ast, variance_oli, variance_opc, variance_end)

final_matrix_variance <- final_matrix_variance %>%
  mutate(across(where(is.numeric), ~ format(., scientific = TRUE, digits = 15)))

write.xlsx(final_matrix_variance, file = paste0(work_dir, "vp/variance_vp_sn_JNI_rev1.xlsx", rowNames = FALSE))

Session info

sessionInfo()
## R version 4.1.2 (2021-11-01)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: CentOS Stream 8
## 
## Matrix products: default
## BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.15.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] parallel  stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] ggrepel_0.9.5            ggbeeswarm_0.6.0         reshape2_1.4.4          
##  [4] doParallel_1.0.17        iterators_1.0.14         foreach_1.5.2           
##  [7] openxlsx_4.2.8           Matrix_1.6-1.1           ggeasy_0.1.3            
## [10] variancePartition_1.24.0 BiocParallel_1.28.3      limma_3.50.3            
## [13] ggpubr_0.6.0             lubridate_1.9.3          forcats_1.0.0           
## [16] stringr_1.5.1            dplyr_1.1.4              purrr_1.0.2             
## [19] readr_2.1.5              tidyr_1.3.1              tibble_3.2.1            
## [22] ggplot2_3.5.0            tidyverse_2.0.0         
## 
## loaded via a namespace (and not attached):
##  [1] nlme_3.1-153        bitops_1.0-7        pbkrtest_0.5.1     
##  [4] progress_1.2.3      tools_4.1.2         backports_1.4.1    
##  [7] bslib_0.7.0         utf8_1.2.4          R6_2.5.1           
## [10] KernSmooth_2.23-20  vipor_0.4.5         BiocGenerics_0.40.0
## [13] colorspace_2.1-0    withr_3.0.0         tidyselect_1.2.1   
## [16] prettyunits_1.2.0   compiler_4.1.2      cli_3.6.2          
## [19] Biobase_2.54.0      labeling_0.4.3      sass_0.4.9         
## [22] caTools_1.18.2      scales_1.3.0        digest_0.6.35      
## [25] minqa_1.2.6         rmarkdown_2.26      pkgconfig_2.0.3    
## [28] htmltools_0.5.8.1   lme4_1.1-28         highr_0.10         
## [31] fastmap_1.1.1       rlang_1.1.3         rstudioapi_0.16.0  
## [34] farver_2.1.1        jquerylib_0.1.4     generics_0.1.3     
## [37] jsonlite_1.8.8      gtools_3.9.4        zip_2.2.0          
## [40] car_3.1-2           magrittr_2.0.3      Rcpp_1.0.12        
## [43] munsell_0.5.1       fansi_1.0.6         abind_1.4-5        
## [46] lifecycle_1.0.4     stringi_1.8.3       yaml_2.3.8         
## [49] carData_3.0-5       MASS_7.3-54         gplots_3.1.3       
## [52] plyr_1.8.9          grid_4.1.2          crayon_1.5.2       
## [55] lattice_0.20-45     splines_4.1.2       hms_1.1.3          
## [58] knitr_1.46          pillar_1.9.0        boot_1.3-28        
## [61] ggsignif_0.6.4      codetools_0.2-18    glue_1.7.0         
## [64] evaluate_0.23       vctrs_0.6.5         nloptr_2.0.3       
## [67] tzdb_0.4.0          gtable_0.3.4        cachem_1.0.8       
## [70] xfun_0.43           broom_1.0.5         rstatix_0.7.2      
## [73] beeswarm_0.4.0      timechange_0.3.0