Last updated: 2023-07-14

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Knit directory: Cardiotoxicity/

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Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.


These are the previous versions of the repository in which changes were made to the R Markdown (analysis/variance_scrip.Rmd) and HTML (docs/variance_scrip.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File Version Author Date Message
Rmd fcc6805 reneeisnowhere 2023-07-14 adding link to variance scrip for Michelle

library(tidyverse)
── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
✔ dplyr     1.1.2     ✔ readr     2.1.4
✔ forcats   1.0.0     ✔ stringr   1.5.0
✔ ggplot2   3.4.2     ✔ tibble    3.2.1
✔ lubridate 1.9.2     ✔ tidyr     1.3.0
✔ purrr     1.0.1     
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
library(ggpubr)
library(ggsignif)

initial calculations and data loading

by individual

by drug

plot by indv

plot by drug

mean_vardrug1 <- read.csv("data/mean_vardrug1.csv")


drug_frame<- mean_vardrug1 %>% 
  rownames_to_column(var = "entrezid") %>% 
  pivot_longer(cols = mean.Da.3:var.Ve.24, names_to = "short", values_to = "values") %>% 
  separate(short, into=c("calc","treatment","time")) %>% 
  mutate(treatment= factor(treatment, levels = c("Do","Ep","Da","Mi","Tr","Ve"),labels = c("DOX","EPI","DNR","MTX","TRZ","VEH"))) %>% 
  mutate(time= factor(time, levels = c("3","24"), labels= c("3 hours","24 hours"))) %>% 
  group_by(treatment, time, calc) %>% 
  as.data.frame



drug_frame %>% 
  filter(calc!="mean") %>% 
  ggplot(., aes(x= treatment, y=values))+
  geom_boxplot()+
  geom_signif(comparisons =list(c("DOX","VEH"),
                                c("EPI","VEH"),
                                c("DNR","VEH"),
                                c("MTX","VEH"),
                                c("TRZ","VEH")),
              test= "t.test",
              map_signif_level=FALSE,
              textsize =4,
              step_increase = 0.1)+
  facet_wrap(~time)+
  ggtitle("var")+
  ylim(0,0.5)
Warning: Removed 23214 rows containing non-finite values (`stat_boxplot()`).
Warning: Removed 23214 rows containing non-finite values (`stat_signif()`).
Warning: Removed 30 rows containing missing values (`geom_signif()`).

drug_frame %>% 
  filter(calc!="mean") %>% 
  ggplot(., aes(x= treatment, y=values))+
  geom_boxplot()+
  geom_signif(comparisons =list(c("DOX","VEH"),
                                c("EPI","VEH"),
                                c("DNR","VEH"),
                                c("MTX","VEH"),
                                c("TRZ","VEH")),
              test= "t.test",
              map_signif_level=FALSE,
              textsize =4,
              step_increase = 0.1)+
  facet_wrap(~time)+
  ggtitle("var")#+

  # ylim(0,0.5)

drug_frame %>% 
  filter(calc!="var") %>% 
  ggplot(., aes(x= treatment, y=values))+
  geom_boxplot()+
  geom_signif(comparisons =list(c("TRZ","VEH"),
                                c("MTX","VEH"),
                                c("DNR","VEH"),
                                c("EPI","VEH"),
                                c("DOX","VEH")),
              test= "t.test",
              map_signif_level=FALSE,
              textsize =4,
              step_increase = 0.05)+
  facet_wrap(.~time)+
  ggtitle("Means")+
  ylim(0,18)
Warning: Removed 3297 rows containing non-finite values (`stat_boxplot()`).
Warning: Removed 3297 rows containing non-finite values (`stat_signif()`).

Calculations without Vehicle

by indvidual and drug

plot by indv no veh

plot by drug no veh

drug_noveh1 <- read.csv("data/drug_noveh1.csv",row.names = 1)

drug_frame_nv <- drug_noveh1 %>% 
  rownames_to_column(var = "entrezid") %>% 
  pivot_longer(cols = mean.Da.3:var.Tr.24, names_to = "short", values_to = "values") %>% 
  separate(short, into=c("calc","treatment","time")) %>% 
  mutate(treatment= factor(treatment, levels = c("Do","Ep","Da","Mi","Tr","Ve"),labels = c("DOX","EPI","DNR","MTX","TRZ","VEH"))) %>% 
  mutate(time= factor(time, levels = c("3","24"), labels= c("3 hours","24 hours"))) %>% 
  group_by(treatment, time, calc) %>% 
  as.data.frame

ggplot(drug_frame_nv, aes(x= treatment, y=values))+
  geom_boxplot()+
  stat_compare_means(method= "anova",  label.x =2)+
  facet_wrap(time~calc, scales = "free_y")

mean_vardrug1 <- read.csv("data/mean_vardrug1.csv",row.names = 1)
my_exp_genes <- read.csv("data/backGL.txt")
GTEx_genes <- read.csv("data/GTEx_gene_list.csv",row.names = 1)
GTEx <- intersect(GTEx_genes$entrezgene_id,my_exp_genes$ENTREZID)
knowles5 <-readRDS("output/knowles5.RDS")


drug_frame2<- mean_vardrug1 %>% 
  rownames_to_column(var = "entrezid") %>% 
  filter(entrezid %in%knowles5$entrezgene_id) %>% 
  pivot_longer(cols = mean.Da.3:var.Ve.24, names_to = "short", values_to = "values") %>% 
  separate(short, into=c("calc","treatment","time")) %>% 
  mutate(treatment= factor(treatment, levels = c("Do","Ep","Da","Mi","Tr","Ve"),labels = c("DOX","EPI","DNR","MTX","TRZ","VEH"))) %>% 
  mutate(time= factor(time, levels = c("3","24"), labels= c("3 hours","24 hours"))) %>% 
  group_by(treatment, time, calc) %>% 
  as.data.frame

ggplot(drug_frame2, aes(x= treatment, y=values))+
  geom_boxplot()+
  geom_signif(comparisons =list(c("DOX","VEH"),
                                c("EPI","VEH"),
                                c("DNR","VEH"),
                                c("MTX","VEH"),
                                c("TRZ","VEH")),
              test= "t.test",
              map_signif_level=TRUE,
              textsize =4,
              step_increase = 0.1)+
  # stat_compare_means(method= "anova", label.y=15, label.x =2)+
  facet_wrap(time~calc, scales = "free_y")

  drug_frame2 %>% 
  filter(calc!="mean") %>% 
  ggplot(., aes(x= treatment, y=values))+
  geom_boxplot()+
  geom_signif(comparisons =list(c("DOX","VEH"),
                                c("EPI","VEH"),
                                c("DNR","VEH"),
                                c("MTX","VEH"),
                                c("TRZ","VEH")),
              test= "t.test",
              map_signif_level=TRUE,
              textsize =4,
              step_increase = 0.1)+
  facet_wrap(~time)+
  ggtitle("var using response eGenes")+
  ylim(0,1.0)
Warning: Removed 146 rows containing non-finite values (`stat_boxplot()`).
Warning: Removed 146 rows containing non-finite values (`stat_signif()`).
Warning: Removed 30 rows containing missing values (`geom_signif()`).

drug_frame2 %>% 
  filter(calc!="var") %>% 
  ggplot(., aes(x= treatment, y=values))+
  geom_boxplot()+
  geom_signif(comparisons =list(c("TRZ","VEH"),
                                c("MTX","VEH"),
                                c("DNR","VEH"),
                                c("EPI","VEH"),
                                c("DOX","VEH")),
              test= "t.test",
              map_signif_level=TRUE,
              textsize =4,
              step_increase = 0.05)+
  facet_wrap(.~time)+
  ggtitle("Means using response eGenes")+
  ylim(0,18)
Warning: Removed 9 rows containing non-finite values (`stat_boxplot()`).
Warning: Removed 9 rows containing non-finite values (`stat_signif()`).


sessionInfo()
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] ggsignif_0.6.4  ggpubr_0.6.0    lubridate_1.9.2 forcats_1.0.0  
 [5] stringr_1.5.0   dplyr_1.1.2     purrr_1.0.1     readr_2.1.4    
 [9] tidyr_1.3.0     tibble_3.2.1    ggplot2_3.4.2   tidyverse_2.0.0
[13] workflowr_1.7.0

loaded via a namespace (and not attached):
 [1] gtable_0.3.3      xfun_0.39         bslib_0.5.0       processx_3.8.1   
 [5] rstatix_0.7.2     callr_3.7.3       tzdb_0.4.0        vctrs_0.6.3      
 [9] tools_4.3.1       ps_1.7.5          generics_0.1.3    fansi_1.0.4      
[13] highr_0.10        pkgconfig_2.0.3   lifecycle_1.0.3   compiler_4.3.1   
[17] farver_2.1.1      git2r_0.32.0      munsell_0.5.0     getPass_0.2-2    
[21] carData_3.0-5     httpuv_1.6.11     htmltools_0.5.5   sass_0.4.6       
[25] yaml_2.3.7        later_1.3.1       pillar_1.9.0      car_3.1-2        
[29] jquerylib_0.1.4   whisker_0.4.1     cachem_1.0.8      abind_1.4-5      
[33] tidyselect_1.2.0  digest_0.6.33     stringi_1.7.12    labeling_0.4.2   
[37] rprojroot_2.0.3   fastmap_1.1.1     grid_4.3.1        colorspace_2.1-0 
[41] cli_3.6.1         magrittr_2.0.3    utf8_1.2.3        broom_1.0.5      
[45] withr_2.5.0       scales_1.2.1      promises_1.2.0.1  backports_1.4.1  
[49] timechange_0.2.0  rmarkdown_2.23    httr_1.4.6        hms_1.1.3        
[53] evaluate_0.21     knitr_1.43        rlang_1.1.1       Rcpp_1.0.11      
[57] glue_1.6.2        rstudioapi_0.15.0 jsonlite_1.8.7    R6_2.5.1         
[61] fs_1.6.2