Last updated: 2023-07-28

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Knit directory: Cardiotoxicity/

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Figure 3

Top2i drugs affect cardiomyocyte viability in a dose dependent manner.

A. PCA of log2 cpm

<environment: R_GlobalEnv>

B. Top2\(\beta\) expression

cpm_boxplot <-function(cpmcounts, GOI,brewer_palette, fill_colors, ylab) {
  ##GOI needs to be ENTREZID
  df <- cpmcounts
    df_plot <- df %>% 
      dplyr::filter(rownames(.)==GOI) %>%
      pivot_longer(everything(),
                   names_to = "treatment",values_to = "counts") %>%
      separate(treatment, c("drug","indv","time")) %>%
      mutate(time=factor(time, levels =c("3h", "24h"), labels=c("3 hours","24 hours"))) %>%
      mutate(indv=factor(indv, levels = c(1,2,3,4,5,6))) %>%
      mutate(drug =case_match(drug, "Da"~"DNR",
                          "Do"~"DOX",
                          "Ep"~"EPI",
                          "Mi"~"MTX",
                          "Tr"~"TRZ",
                          "Ve"~"VEH", .default = drug)) %>%
  mutate(drug=factor(drug, levels = c('DOX','EPI','DNR','MTX','TRZ','VEH')))
    plot <- ggplot2::ggplot(df_plot, aes(x=drug, y=counts))+
      geom_boxplot(position="identity",aes(fill=drug))+
      geom_point(aes(col=indv, size=2, alpha=0.5))+
      guides(alpha= "none", size= "none")+
      scale_color_brewer(palette = brewer_palette, name = "Individual")+
      scale_fill_manual(values=fill_colors, name="treatment")+
      facet_wrap("time", nrow=1, ncol=2)+
      theme_bw()+
      ylab(ylab)+
      xlab("")+
      theme(strip.background = element_rect(fill = "white",linetype=1, linewidth = 0.5),
          plot.title = element_text(size=12,hjust = 0.5,face="bold"),
          axis.title = element_text(size = 10, color = "black"),
          
          axis.line = element_line(linewidth = 1.0),
          axis.text.x = element_blank(),
          strip.text.x = element_text(face = "bold"))
    print(plot)
}

B. Top2\(\alpha\) expression


R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default


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

time zone: America/Chicago
tzcode source: internal

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

other attached packages:
 [1] edgeR_3.42.4        limma_3.56.2        broom_1.0.5        
 [4] RColorBrewer_1.1-3  ggsignif_0.6.4      cowplot_1.1.1      
 [7] drc_3.0-1           MASS_7.3-60         BiocGenerics_0.46.0
[10] tinytex_0.45        lubridate_1.9.2     forcats_1.0.0      
[13] stringr_1.5.0       dplyr_1.1.2         purrr_1.0.1        
[16] readr_2.1.4         tidyr_1.3.0         tibble_3.2.1       
[19] ggplot2_3.4.2       tidyverse_2.0.0     car_3.1-2          
[22] carData_3.0-5       workflowr_1.7.0    

loaded via a namespace (and not attached):
 [1] tidyselect_1.2.0  farver_2.1.1      fastmap_1.1.1     TH.data_1.1-2    
 [5] promises_1.2.0.1  digest_0.6.33     timechange_0.2.0  lifecycle_1.0.3  
 [9] survival_3.5-5    processx_3.8.2    magrittr_2.0.3    compiler_4.3.1   
[13] rlang_1.1.1       sass_0.4.7        tools_4.3.1       plotrix_3.8-2    
[17] utf8_1.2.3        yaml_2.3.7        knitr_1.43        labeling_0.4.2   
[21] multcomp_1.4-25   abind_1.4-5       withr_2.5.0       grid_4.3.1       
[25] fansi_1.0.4       git2r_0.32.0      colorspace_2.1-0  scales_1.2.1     
[29] gtools_3.9.4      cli_3.6.1         mvtnorm_1.2-2     rmarkdown_2.23   
[33] ragg_1.2.5        generics_0.1.3    rstudioapi_0.15.0 httr_1.4.6       
[37] tzdb_0.4.0        cachem_1.0.8      splines_4.3.1     vctrs_0.6.3      
[41] Matrix_1.6-0      sandwich_3.0-2    jsonlite_1.8.7    callr_3.7.3      
[45] hms_1.1.3         ggrepel_0.9.3     systemfonts_1.0.4 locfit_1.5-9.8   
[49] jquerylib_0.1.4   glue_1.6.2        codetools_0.2-19  ps_1.7.5         
[53] stringi_1.7.12    gtable_0.3.3      later_1.3.1       munsell_0.5.0    
[57] pillar_1.9.0      htmltools_0.5.5   R6_2.5.1          textshaping_0.3.6
[61] rprojroot_2.0.3   evaluate_0.21     lattice_0.21-8    highr_0.10       
[65] backports_1.4.1   httpuv_1.6.11     bslib_0.5.0       Rcpp_1.0.11      
[69] whisker_0.4.1     xfun_0.39         fs_1.6.3          zoo_1.8-12       
[73] getPass_0.2-2     pkgconfig_2.0.3