Boxplot - IL15 microglial expression by diagnosis

IL15 expression in microglia by diagnosis at the time of death: AD (Alzheimer’s Disease), MCI (Mild cognitive impairment) and NCI (no cognitive impairment).

IL15 expression by diagnosis

#celltype_exp$mic[1:5, 1:5]
cell_i = "mic"

dt_res = as.data.frame(celltype_exp[[cell_i]], check.names = F) 
dt_res_selected = dt_res[rownames(dt_res) %in% ensembls, ]

# long format for the plot
dt_res_selected_l = dt_res_selected %>% 
  rownames_to_column("ensembl") %>%
  pivot_longer(-ensembl, values_to = "expression", names_to = "projid") %>%
  mutate(celltype = cell_i)

# join to get the gene_name
dt_res_selected_l = dt_res_selected_l %>%
  left_join(cytokines, by = "ensembl")

# join to get the phenotype 
dt_res_selected_l_meta = dt_res_selected_l %>% 
  left_join(pheno_SN, by = "projid") %>%
  filter(symbol == "IL15")

# By diagnosis 
dt_res_selected_l_meta$cogdx_3grp[dt_res_selected_l_meta$cogdx_3grp == 0] <- "NCI"
dt_res_selected_l_meta$cogdx_3grp[dt_res_selected_l_meta$cogdx_3grp == 1] <- "MCI"
dt_res_selected_l_meta$cogdx_3grp[dt_res_selected_l_meta$cogdx_3grp == 2] <- "AD"

dt_res_selected_l_meta$cogdx_3grp = as.factor(dt_res_selected_l_meta$cogdx_3grp)
names(dt_res_selected_l_meta)[names(dt_res_selected_l_meta) == 'cogdx_3grp'] <- 'Diagnosis'

my_comparisons = list(c("AD", "NCI"),
                      c("AD", "MCI"),
                      c("MCI", "NCI"))

p <- ggplot(na.omit(dt_res_selected_l_meta[, c("Diagnosis", "expression", "symbol")]), aes(x = Diagnosis, y = expression, fill = Diagnosis)) + 
  geom_boxplot(outlier.shape = NA) + 
  geom_jitter(position = position_jitter(width = 0.2), size = 1, alpha = 0.7) + 
  stat_compare_means(comparisons = my_comparisons, method = "t.test", size = 7, bracket.size = 0.65) +
  facet_wrap(~ symbol, scales = "free") + 
  scale_fill_manual(values = c("AD" = "#BB5566", "MCI" = "#DDAA33", "NCI" = "#004488")) + 
  labs(y = "IL15 expression in microglia", x = "Final consensus diagnosis") + 
  theme_classic()+
  theme(
    text = element_text(size = 22),
    axis.title = element_text(size = 22),
    axis.text = element_text(size = 18),
    legend.position = "none"
  )

print(p)

# Save to PDF
pdf(file = paste0("boxplot_IL15_mic_T047", ".pdf"), width = 8, height = 8)
print(p)
dev.off()

## png 
##   2

# Save to PNG
png(file = paste0("boxplot_IL15_mic_T047", ".png"), width = 2000, height = 2800, res = 300)
print(p)
dev.off()

## png 
##   2

Session info

sessionInfo()

## R version 4.3.2 (2023-10-31 ucrt)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 11 x64 (build 26100)
## 
## Matrix products: default
## 
## 
## locale:
## [1] LC_COLLATE=Portuguese_Brazil.utf8  LC_CTYPE=Portuguese_Brazil.utf8   
## [3] LC_MONETARY=Portuguese_Brazil.utf8 LC_NUMERIC=C                      
## [5] LC_TIME=Portuguese_Brazil.utf8    
## 
## time zone: America/Sao_Paulo
## tzcode source: internal
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] readxl_1.4.3    ggsignif_0.6.4  ggeasy_0.1.4    ggpubr_0.6.0   
##  [5] lubridate_1.9.3 forcats_1.0.0   stringr_1.5.1   purrr_1.0.2    
##  [9] tidyr_1.3.1     tibble_3.2.1    tidyverse_2.0.0 ggplot2_3.5.0  
## [13] readr_2.1.5     rstatix_0.7.2   dplyr_1.1.4    
## 
## loaded via a namespace (and not attached):
##  [1] sass_0.4.9        utf8_1.2.4        generics_0.1.3    stringi_1.8.3    
##  [5] hms_1.1.3         digest_0.6.36     magrittr_2.0.3    evaluate_0.24.0  
##  [9] grid_4.3.2        timechange_0.3.0  fastmap_1.2.0     cellranger_1.1.0 
## [13] jsonlite_1.8.8    backports_1.4.1   fansi_1.0.6       scales_1.3.0     
## [17] jquerylib_0.1.4   abind_1.4-5       cli_3.6.2         rlang_1.1.3      
## [21] munsell_0.5.1     withr_3.0.1       cachem_1.1.0      yaml_2.3.10      
## [25] tools_4.3.2       tzdb_0.4.0        colorspace_2.1-0  broom_1.0.6      
## [29] vctrs_0.6.5       R6_2.5.1          lifecycle_1.0.4   car_3.1-2        
## [33] pkgconfig_2.0.3   pillar_1.9.0      bslib_0.8.0       gtable_0.3.5     
## [37] glue_1.7.0        highr_0.11        xfun_0.46         tidyselect_1.2.1 
## [41] rstudioapi_0.16.0 knitr_1.48        farver_2.1.1      htmltools_0.5.8.1
## [45] labeling_0.4.3    rmarkdown_2.27    carData_3.0-5     compiler_4.3.2