Figure1
ERM
2023-06-16
Last updated: 2023-06-16
Checks: 7 0
Knit directory: Cardiotoxicity/
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library(car)
#library(dr4pl) no longer used
library(tidyverse)
library(tinytex)
library(BiocGenerics)
library(data.table)
library(drc)
# library(Hmisc)
library(cowplot)
# library(grid)
library(ggsignif)
library(RColorBrewer)
library(broom)Figure 1
Top2i drugs affect cardiomyocyte viability in a dose dependent manner.
A. Project Overview
things to note about this image so far: Need to import into illustrator. Goal is to have colors changes on Drugs from sick purple and jaundice yellow, to a red tone and a blue tone for non-ACs. I also want to change to add a time line of treatment.
B. Example Dose response curves from 48 hour drug exposure.
daplot <- readRDS("output/daplot.RDS")
dxplot <- readRDS("output/dxplot.RDS")
epplot<- readRDS("output/epplot.RDS")
mtplot<- readRDS("output/mtplot.RDS")
trplot<- readRDS("output/trplot.RDS")
veplot<- readRDS("output/veplot.RDS")
plan2 <- cowplot::plot_grid(daplot,dxplot,epplot,mtplot, trplot,veplot,ncol =3)
print(plan2)
Lines are a log-logistic regression of the mean from quadruplicates at 8
separate concentrations for each condition, except (trastuzmab)TRZ,
which is 7 concentrations.
C. 48 hour 50% lethal dose plot
drug_palc <- c("#8B006D","#DF707E","#F1B72B", "#3386DD","#707031","#41B333")
BC_cell_lines <- read.csv("data/BC_cell_lines.csv",row.names = 1)
avgLD50 <- readRDS("data/avgLD50.RDS")
graphLD50 <-
avgLD50 %>%
mutate(Treatment = case_match (Treatment, "Daun"~"Daunorubicin",
"Doxo"~"Doxorubicin",
"Epi"~"Epirubicin",
"Mito"~"Mitoxantrone",
"Tras"~"Trastuzumab",
"Veh"~ "Vehicle",
.default= Treatment)) %>%
mutate(indv= factor(indv)) %>%
ggplot(., (aes(x = (Treatment), y = log10(LD50)))) +
geom_boxplot(position = "identity", aes(fill=Treatment))+
geom_point(aes(color = indv,
size = 5,alpha = 0.5)) +
ggtitle(expression("Experimentally-derived LD"[50]*"s from treated cardiomyocytes"))+
xlab("Treatment")+
ylab(bquote('Log'[10]~ 'LD'[50]~'in '*mu*M))+
scale_color_brewer(palette = "Dark2",
name = "Individual",
labels = c("1","2","3","4","5","6"))+
ylim(-2,2)+
scale_fill_manual(values=drug_palc)+
theme_bw() +
theme(plot.title = element_text(hjust =0.5, size = 18))+
guides(alpha ="none", size = "none")+
#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"))
graphLD50
## D. Breast Cancer cell line 50% lethal dose plot
graphBC <- BC_cell_lines %>%
mutate(Cell_line= factor(Cell_line)) %>%
pivot_longer(.,col=!Cell_line,names_to = 'Treatment',values_to = 'LD50') %>%
ggplot(., (aes(x = (Treatment), y = log10(LD50)))) +
geom_boxplot(position = "identity",aes(fill=Treatment))+
geom_point(aes(color = Cell_line,
size = 5,alpha = 0.5)) +
ggtitle(expression("Breast cancer cell line reported LD"[50]*"s"))+
xlab("")+
ylab(bquote('Log'[10]~ 'LD'[50]~'in '*mu*M))+
scale_color_brewer(palette = "Spectral",
name = "Cell lines")+
scale_fill_manual(values=drug_palc)+
ylim(-2,2)+
theme_bw() +
theme(plot.title = element_text(hjust =0.5, size = 18))+
guides(alpha ="none", size = "none", fill= "none")+
#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"))
graphBC
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
loaded via a namespace (and not attached):
[1] httr_1.4.6 sass_0.4.6 jsonlite_1.8.5 splines_4.2.2
[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 mgcv_1.8-42 farver_2.1.1 generics_0.1.3
[33] TH.data_1.1-2 cachem_1.0.8 withr_2.5.0 cli_3.6.1
[37] survival_3.5-5 magrittr_2.0.3 evaluate_0.21 ps_1.7.5
[41] fs_1.6.2 fansi_1.0.4 nlme_3.1-162 tools_4.2.2
[45] hms_1.1.3 lifecycle_1.0.3 multcomp_1.4-24 munsell_0.5.0
[49] plotrix_3.8-2 callr_3.7.3 compiler_4.2.2 jquerylib_0.1.4
[53] rlang_1.1.1 grid_4.2.2 rstudioapi_0.14 labeling_0.4.2
[57] rmarkdown_2.22 gtable_0.3.3 codetools_0.2-19 abind_1.4-5
[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 stringi_1.7.12 Rcpp_1.0.10
[69] vctrs_0.6.3 tidyselect_1.2.0 xfun_0.39