Cytokines

This list of cytokines was constructed based on the supplementary material from Cui et al. Nature, 2020 e Santoso Nucleic Acids Research et al., 2020.

# upload gene list
file_path <- "C:/Users/beker/OneDrive/Documentos/Mestrado/GitHub/Cytokines/list_cytokines/T023/list_cytokines_T023.xlsx"
cytokines <- read_excel(file_path)
# Reducing cytokine families
cytokines <- cytokines %>%
  mutate(family = case_when(
    family %in% c("IL-10", "IL-17", "IL-1", "Common γ chain/IL-13/TSLP", "IL-6/IL-12", "IL10", "IL32", "Common β chain") ~ "Interleukine",
    TRUE ~ family
  ))

createDT(cytokines)
# Saving excel
write.xlsx(cytokines, file = "C:/Users/beker/OneDrive/Documentos/Mestrado/GitHub/Cytokines/list_cytokines/T049/new_cytokines_families_T049.xlsx", row.names = FALSE)
# Frequency of genes 'family'
family_counts <- sort(table(cytokines$family), decreasing = TRUE)

# Barplot
bar_plot <- barplot(family_counts,
                    main = "Cytokine Genes Annotated by Family",
                    xlab = "Family",
                    ylab = "Number of genes",
                    col = "skyblue",
                    axisnames = FALSE,
                    ylim = c(0, max(family_counts) * 1.25))  # Increase the top margin by 10%) 

# Rotacionar as legendas do eixo x em 45 graus
text(x = bar_plot + 0.1, y = par("usr")[3] - 1.3, labels = names(family_counts), srt = 25, adj = c(1, 1.25), xpd = TRUE, cex = 1)

print(bar_plot)

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] openxlsx_4.2.6.1 readxl_1.4.3     lubridate_1.9.3  forcats_1.0.0   
##  [5] stringr_1.5.1    dplyr_1.1.4      purrr_1.0.2      readr_2.1.5     
##  [9] tidyr_1.3.1      tibble_3.2.1     ggplot2_3.5.0    tidyverse_2.0.0 
## 
## 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    zip_2.3.1         fansi_1.0.6       crosstalk_1.2.1  
## [17] scales_1.3.0      jquerylib_0.1.4   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  DT_0.33          
## [29] vctrs_0.6.5       R6_2.5.1          lifecycle_1.0.4   htmlwidgets_1.6.4
## [33] pkgconfig_2.0.3   pillar_1.9.0      bslib_0.8.0       gtable_0.3.5     
## [37] glue_1.7.0        Rcpp_1.0.12       highr_0.11        xfun_0.46        
## [41] tidyselect_1.2.1  rstudioapi_0.16.0 knitr_1.48        htmltools_0.5.8.1
## [45] rmarkdown_2.27    compiler_4.3.2