Figure2
ERM
2023-07-07
Last updated: 2023-07-07
Checks: 7 0
Knit directory: Cardiotoxicity/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 2440452 | reneeisnowhere | 2023-07-07 | correct Trop I |
| html | b3dc281 | reneeisnowhere | 2023-07-07 | Build site. |
| Rmd | e5cbe6d | reneeisnowhere | 2023-07-07 | update exports |
| html | 32ba3b4 | reneeisnowhere | 2023-07-06 | Build site. |
| Rmd | b94a1e0 | reneeisnowhere | 2023-07-06 | adding fig 2 updates |
| html | 2379232 | reneeisnowhere | 2023-06-27 | Build site. |
| Rmd | 9719ccd | reneeisnowhere | 2023-06-27 | updated order on graphs |
| html | c382ce9 | reneeisnowhere | 2023-06-16 | Build site. |
| Rmd | ac33c8f | reneeisnowhere | 2023-06-16 | adding figure 2 |
| Rmd | 5253904 | reneeisnowhere | 2023-06-16 | adding figure 2 |
Figure 2
Minimal cellular stress is induced following 24 hours of treatment
A. Lactate dehydrogenase release at 24 hours
drug_pal <- c("#41B333","#8B006D","#DF707E","#F1B72B", "#3386DD","#707031")
level_order2 <- c('75','87','77','79','78','71')
drug_pal_fact <- c("#8B006D","#DF707E","#F1B72B", "#3386DD","#707031","#41B333")
RNAnormlist <- read.csv("output/TNNI_LDH_RNAnormlist.txt",row.names = 1)
RNAnormlist %>%
mutate(Drug = factor(Drug, levels = c( "DOX",
"EPI",
"DNR",
"MTX",
"TRZ",
"VEH"))) %>%
mutate(indv= factor(indv,levels= level_order2)) %>%
ggplot(., aes(x=Drug, y=rldh))+
geom_boxplot(position = "identity", fill = drug_pal_fact)+
geom_point(aes(col=indv, size =3,alpha=0.5))+
geom_signif(comparisons =list(c("VEH","DOX"),
c("VEH","EPI"),
c("VEH","DNR"),
c("VEH","MTX"),
c("VEH","TRZ")),
test="t.test",
map_signif_level=TRUE,
textsize =4,
step_increase = 0.1)+
theme_classic()+
guides(size = "none",alpha="none")+
scale_color_brewer(palette = "Dark2", name = "Individual")+
xlab("")+
ylab("Relative LDH activity ")+
ggtitle("Lactate dehydrogenase release at 24 hours")+
theme_classic()+
theme(strip.background = element_rect(fill = "transparent")) +
theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
legend.position = "none",
axis.title = element_text(size = 15, color = "black"),
axis.ticks = element_line(linewidth = 1.5),
axis.line = element_line(linewidth = 1.5),
axis.text = element_text(size = 12, color = "black", angle = 0),
strip.text.x = element_text(size = 15, color = "black", face = "bold"))
ggsave("output/Figures/LDH24h.eps",width = 4, height =6, units = "in")C. Troponin I release
RNAnormlist %>%
mutate(Drug = factor(Drug, levels = c( "DOX",
"EPI",
"DNR",
"MTX",
"TRZ",
"VEH"))) %>%
mutate(indv= factor(indv,levels= level_order2)) %>%
ggplot(., aes(x=Drug, y=rtnni))+
geom_boxplot(position = "identity", fill = drug_pal_fact)+
geom_point(aes(col=indv, size =3,alpha=0.5))+
geom_signif(comparisons =list(c("VEH","DOX"),
c("VEH","EPI"),
c("VEH","DNR"),
c("VEH","MTX"),
c("VEH","TRZ")),
test="t.test",
map_signif_level=TRUE,
textsize =4,
step_increase = 0.1)+
theme_classic()+
guides(size = "none",alpha="none")+
scale_color_brewer(palette = "Dark2", name = "Individual")+
xlab("")+
ylab("Relative Troponin I levels ")+
ggtitle("Troponin I release at 24 hours")+
theme_classic()+
theme(strip.background = element_rect(fill = "transparent")) +
theme(plot.title = element_text(size = rel(1.5), hjust = 0.5),
legend.position = "none",
axis.title = element_text(size = 15, color = "black"),
axis.ticks = element_line(linewidth = 1.5),
axis.line = element_line(linewidth = 1.5),
axis.text = element_text(size = 12, color = "black", angle = 0),
strip.text.x = element_text(size = 15, color = "black", face = "bold"))
ggsave("output/Figures/LDH24h.eps",width = 4, height =6, units = "in")
sessionInfo()R version 4.2.2 (2022-10-31 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
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] broom_1.0.5 RColorBrewer_1.1-3 ggsignif_0.6.4
[4] cowplot_1.1.1 drc_3.0-1 MASS_7.3-60
[7] data.table_1.14.8 BiocGenerics_0.42.0 tinytex_0.45
[10] lubridate_1.9.2 forcats_1.0.0 stringr_1.5.0
[13] dplyr_1.1.2 purrr_1.0.1 readr_2.1.4
[16] tidyr_1.3.0 tibble_3.2.1 ggplot2_3.4.2
[19] tidyverse_2.0.0 car_3.1-2 carData_3.0-5
[22] workflowr_1.7.0
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[5] gtools_3.9.4 bslib_0.5.0 getPass_0.2-2 highr_0.10
[9] yaml_2.3.7 pillar_1.9.0 backports_1.4.1 lattice_0.21-8
[13] glue_1.6.2 digest_0.6.31 promises_1.2.0.1 colorspace_2.1-0
[17] sandwich_3.0-2 htmltools_0.5.5 httpuv_1.6.11 Matrix_1.5-4.1
[21] pkgconfig_2.0.3 mvtnorm_1.2-2 scales_1.2.1 processx_3.8.1
[25] whisker_0.4.1 later_1.3.1 tzdb_0.4.0 timechange_0.2.0
[29] git2r_0.32.0 farver_2.1.1 generics_0.1.3 TH.data_1.1-2
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[37] magrittr_2.0.3 evaluate_0.21 ps_1.7.5 fs_1.6.2
[41] fansi_1.0.4 textshaping_0.3.6 tools_4.2.2 hms_1.1.3
[45] lifecycle_1.0.3 multcomp_1.4-24 munsell_0.5.0 plotrix_3.8-2
[49] callr_3.7.3 compiler_4.2.2 jquerylib_0.1.4 systemfonts_1.0.4
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[61] R6_2.5.1 zoo_1.8-12 knitr_1.43 fastmap_1.1.1
[65] utf8_1.2.3 rprojroot_2.0.3 ragg_1.2.5 stringi_1.7.12
[69] Rcpp_1.0.10 vctrs_0.6.3 tidyselect_1.2.0 xfun_0.39