Last updated: 2023-07-19
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Knit directory: Cardiotoxicity/
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Rmd | f3ce7e9 | reneeisnowhere | 2023-07-19 | updated LD50 plot |
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library(car)
library(tidyverse)
library(tinytex)
library(BiocGenerics)
library(data.table)
library(drc)
library(cowplot)
library(ggsignif)
library(RColorBrewer)
library(broom)
library(ComplexHeatmap)
Top2i drugs affect cardiomyocyte viability in a dose dependent manner.
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.
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")
legend_b <- readRDS("output/legend_b.RDS")
plan2 <- cowplot::plot_grid(daplot,dxplot,epplot,mtplot, trplot,veplot, legend_b,ncol =4)
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.
drug_palc <- c("#8B006D","#DF707E","#F1B72B", "#3386DD","#707031","#41B333")
BC_cell_lines <- read.csv("data/BC_cell_lines.csv",row.names = 1)
LD50_table <- readRDS("data/new_ld50avg.RDS")
LD50_table %>%
mutate(Treatment=factor(Treatment,
levels = c('DOX', 'EPI', 'DNR', 'MTX', 'TRZ', 'VEH'))) %>%
ggplot(., (aes(x = Treatment, y = log10(Estimate)))) +
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")+
geom_signif(comparisons =list(c("DNR","MTX"),
c("DOX","EPI"),
c ("DOX","DNR"),
c("DOX","MTX")),
test="t.test",
map_signif_level=TRUE,
textsize =4,
step_increase = 0.15)+
ylab(bquote('Log'[10]~ 'LD'[50]~'in '*mu*M))+
scale_color_brewer(palette = "Dark2",
name = "Individual")+
ylim(-1.5,3)+
# scale_y_continuous(expand=expansion(.001))+
scale_fill_manual(values=drug_palc, name="Treatment")+
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.x = element_text(size=0,color = "white"),
# axis.text = element_text(size = 12, color = "black", angle = 0),
strip.text.x = element_text(size = 15, color = "black", face = "bold"))
## 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 = 'drug',
values_to = 'LD50') %>%
mutate(drug =case_match(drug, "Daunorubicin"~"DNR",
"Doxorubicin"~"DOX",
"Epirubicin"~"EPI",
"Mitoxantrone"~"MTX",
"Trastuzumab"~"TRZ",
"Vehicle"~"VEH", .default = drug)) %>%
mutate(drug=factor(drug,
levels = c('DOX','EPI','DNR','MTX','TRZ','VEH'))) %>%
ggplot(., (aes(x = (drug), y = log10(LD50)))) +
geom_boxplot(position = "identity",aes(fill=drug))+
geom_point(aes(color = Cell_line,
size = 5,alpha = 0.5)) +
ggtitle(expression("Breast cancer cell line reported LD"[50]*"s"))+
xlab("")+
geom_signif(comparisons =list(c("DOX","EPI"),
c ("DOX","DNR"),
c("DOX","MTX")),
test="t.test",
map_signif_level=TRUE,
textsize =4,
step_increase = 0.15)+
ylab(bquote('Log'[10]~ 'LD'[50]~'in '*mu*M))+
scale_color_brewer(palette = "Spectral",
name = "Cell lines")+
scale_fill_manual(values=drug_palc)+
ylim(-2,2.5)+
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.x = element_text(size=0,color = "white"),
axis.text.y = element_text(size = 12, color = "black", angle = 0),
strip.text.x = element_text(size = 15, color = "black", face = "bold"))
graphBC
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] grid stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] ComplexHeatmap_2.16.0 broom_1.0.5 RColorBrewer_1.1-3
[4] ggsignif_0.6.4 cowplot_1.1.1 drc_3.0-1
[7] MASS_7.3-60 data.table_1.14.8 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] sandwich_3.0-2 rlang_1.1.1 magrittr_2.0.3
[4] clue_0.3-64 GetoptLong_1.0.5 git2r_0.32.0
[7] multcomp_1.4-25 matrixStats_1.0.0 compiler_4.3.1
[10] getPass_0.2-2 mgcv_1.9-0 png_0.1-8
[13] callr_3.7.3 vctrs_0.6.3 pkgconfig_2.0.3
[16] shape_1.4.6 crayon_1.5.2 fastmap_1.1.1
[19] backports_1.4.1 labeling_0.4.2 utf8_1.2.3
[22] promises_1.2.0.1 rmarkdown_2.23 tzdb_0.4.0
[25] ps_1.7.5 xfun_0.39 cachem_1.0.8
[28] jsonlite_1.8.7 highr_0.10 later_1.3.1
[31] parallel_4.3.1 cluster_2.1.4 R6_2.5.1
[34] bslib_0.5.0 stringi_1.7.12 jquerylib_0.1.4
[37] Rcpp_1.0.11 iterators_1.0.14 knitr_1.43
[40] zoo_1.8-12 IRanges_2.34.1 httpuv_1.6.11
[43] Matrix_1.6-0 splines_4.3.1 timechange_0.2.0
[46] tidyselect_1.2.0 rstudioapi_0.15.0 abind_1.4-5
[49] yaml_2.3.7 doParallel_1.0.17 codetools_0.2-19
[52] processx_3.8.1 lattice_0.21-8 withr_2.5.0
[55] evaluate_0.21 survival_3.5-5 circlize_0.4.15
[58] pillar_1.9.0 whisker_0.4.1 foreach_1.5.2
[61] stats4_4.3.1 generics_0.1.3 rprojroot_2.0.3
[64] hms_1.1.3 S4Vectors_0.38.1 munsell_0.5.0
[67] scales_1.2.1 gtools_3.9.4 glue_1.6.2
[70] tools_4.3.1 fs_1.6.2 mvtnorm_1.2-2
[73] plotrix_3.8-2 colorspace_2.1-0 nlme_3.1-162
[76] cli_3.6.1 fansi_1.0.4 gtable_0.3.3
[79] sass_0.4.6 digest_0.6.33 TH.data_1.1-2
[82] farver_2.1.1 rjson_0.2.21 htmltools_0.5.5
[85] lifecycle_1.0.3 httr_1.4.6 GlobalOptions_0.1.2