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Fig_2_Viz.Rmd
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---
title: "Fig_2_Viz"
author: "Troy McDiarmid"
date: "2024-02-13"
output: html_document
---
```{r setup, include=FALSE}
library(tidyverse)
```
```{r}
BB <- read_csv("/Users/troymcdiarmid/Documents/U6_pro_series/Figs/Pub_Figs/Fig2_Final_Figure_Datasets/BB_Edit_Scores_Comparison_Table.csv")
##Calculating correlation between different cell contexts
cor.test(BB$K562, BB$HEK293T)
cor.test(BB$K562, BB$iPSC)
cor.test(BB$iPSC, BB$HEK293T)
##Calculate the median of the standard backbone in each pool and reordering groups for plotting
Standard <- BB %>%
filter(Variant_Type == "Standard") %>%
group_by(BC_Pool) %>%
mutate(K562 = median(K562)) %>%
mutate(HEK293T = median(HEK293T)) %>%
mutate(iPSC = median(iPSC)) %>%
filter(Oligo_Number == 1)
Replacement <- BB %>%
filter(Variant_Type == "Replacement")
Extension <- BB %>%
filter(Variant_Type == "Extension")
BB <- rbind(Extension, Replacement, Standard)
##Correlation plot of edit scores
ggplot(BB, aes(x = log2(K562), y = log2(HEK293T), colour = Variant_Type, size = Variant_Type)) +
geom_point() +
scale_color_manual(values=c("#CCA24C", "#56B4E9", "black")) +
scale_size_manual(values=c(4, 4, 6)) +
scale_x_continuous(labels = scales::number_format(accuracy = 0.1)) +
scale_y_continuous(labels = scales::number_format(accuracy = 0.1)) +
theme_classic() +
theme(axis.line = element_line(colour = 'black', size = 0.8)) +
theme(axis.ticks = element_line(colour = "black", size = 0.8)) +
theme(axis.ticks.length=unit(.2, "cm")) +
labs(title = "", x = "", y = "") +
theme(legend.position = "none") +
theme(text = element_text(family="Arial", colour = "black", size = 39), plot.margin = margin(0, 15, 0, 20))
ggsave("BB_K562_HEK293T_Corr.jpeg", width = 9, height = 7, path = "/Users/troymcdiarmid/Documents/U6_pro_series/Figs/Pub_Figs/")
ggplot(BB, aes(x = log2(K562), y = log2(iPSC), colour = Variant_Type, size = Variant_Type)) +
geom_point() +
scale_color_manual(values=c("#CCA24C", "#56B4E9", "black")) +
scale_size_manual(values=c(4, 4, 6)) +
scale_x_continuous(labels = scales::number_format(accuracy = 0.1)) +
scale_y_continuous(labels = scales::number_format(accuracy = 0.1)) +
theme_classic() +
theme(axis.line = element_line(colour = 'black', size = 0.8)) +
theme(axis.ticks = element_line(colour = "black", size = 0.8)) +
theme(axis.ticks.length=unit(.2, "cm")) +
labs(title = "", x = "", y = "") +
theme(legend.position = "none") +
theme(text = element_text(family="Arial", colour = "black", size = 39), plot.margin = margin(0, 15, 0, 20))
ggsave("BB_K562_iPSC_Corr.jpeg", width = 9, height = 7, path = "/Users/troymcdiarmid/Documents/U6_pro_series/Figs/Pub_Figs/")
ggplot(BB, aes(x = log2(HEK293T), y = log2(iPSC), colour = Variant_Type, size = Variant_Type)) +
geom_point() +
scale_color_manual(values=c("#CCA24C", "#56B4E9", "black")) +
scale_size_manual(values=c(4, 4, 6)) +
scale_x_continuous(labels = scales::number_format(accuracy = 0.1)) +
scale_y_continuous(labels = scales::number_format(accuracy = 0.1)) +
theme_classic() +
theme(axis.line = element_line(colour = 'black', size = 0.8)) +
theme(axis.ticks = element_line(colour = "black", size = 0.8)) +
theme(axis.ticks.length=unit(.2, "cm")) +
labs(title = "", x = "", y = "") +
theme(legend.position = "none") +
theme(text = element_text(family="Arial", colour = "black", size = 39), plot.margin = margin(0, 15, 0, 20))
ggsave("BB_HEK293T_iPSC_Corr.jpeg", width = 9, height = 7, path = "/Users/troymcdiarmid/Documents/U6_pro_series/Figs/Pub_Figs/")
```
```{r}
##Plotting the edit scores by variant class
ggplot(BB, aes(x = log2(K562))) +
geom_histogram(aes(fill = fct_relevel(Variant_Type, "Replacement", "Extension", "Standard")), binwidth = 0.2) +
scale_fill_manual(values=c("#56B4E9", "#CCA24C", "black")) +
scale_y_continuous(breaks = c(0,15,30)) +
theme_classic() +
theme(axis.line = element_line(colour = 'black', size = 0.8)) +
theme(axis.ticks = element_line(colour = "black", size = 0.8)) +
theme(axis.ticks.length=unit(.2, "cm")) +
labs(title = "", x = "", y = "") +
theme(legend.position = "none") +
theme(text = element_text(family="Arial", colour = "black", size = 41))
ggsave("BB_K562_Histo.jpeg", width = 18, height = 4, path = "/Users/troymcdiarmid/Documents/U6_pro_series/Figs/Pub_Figs/")
ggplot(BB, aes(x = log2(HEK293T))) +
geom_histogram(aes(fill = fct_relevel(Variant_Type, "Replacement", "Extension", "Standard")), binwidth = 0.2) +
scale_fill_manual(values=c("#56B4E9", "#CCA24C", "black")) +
scale_y_continuous(breaks = c(0,10,20)) +
theme_classic() +
theme(axis.line = element_line(colour = 'black', size = 0.8)) +
theme(axis.ticks = element_line(colour = "black", size = 0.8)) +
theme(axis.ticks.length=unit(.2, "cm")) +
labs(title = "", x = "", y = "") +
theme(legend.position = "none") +
theme(text = element_text(family="Arial", colour = "black", size = 41))
ggsave("BB_HEK293T_Histo.jpeg", width = 18, height = 4, path = "/Users/troymcdiarmid/Documents/U6_pro_series/Figs/Pub_Figs/")
ggplot(BB, aes(x = log2(iPSC))) +
geom_histogram(aes(fill = fct_relevel(Variant_Type, "Replacement", "Extension", "Standard")), binwidth = 0.2) +
scale_fill_manual(values=c("#56B4E9", "#CCA24C", "black")) +
scale_y_continuous(breaks = c(0,10,20)) +
theme_classic() +
theme(axis.line = element_line(colour = 'black', size = 0.8)) +
theme(axis.ticks = element_line(colour = "black", size = 0.8)) +
theme(axis.ticks.length=unit(.2, "cm")) +
labs(title = "", x = "", y = "") +
theme(legend.position = "none") +
theme(text = element_text(family="Arial", colour = "black", size = 41))
ggsave("BB_iPSC_Histo.jpeg", width = 18, height = 4, path = "/Users/troymcdiarmid/Documents/U6_pro_series/Figs/Pub_Figs/")
```
```{r}
##Isolating the best pegRNAs for plotting
Above_Standard <- BB %>%
filter(Above_Standard == TRUE)
Standard <- BB %>%
filter(Variant_Type == "Standard")
BB_Above_Standard <- rbind(Standard, Above_Standard)
##Converting oligo number to factor for plotting
BB_Above_Standard <- BB_Above_Standard %>%
mutate(Oligo_Number = as.factor(Oligo_Number))
##Calculating fold increase above standard
Standard_BC1 <- Standard %>%
filter(BC_Pool == 1)
BB_Above_Standard_BC1 <- BB_Above_Standard %>%
filter(BC_Pool == 1) %>%
mutate(K562_Fold_Change_Over_Standard = K562/(Standard_BC1$K562)) %>%
mutate(HEK293T_Fold_Change_Over_Standard = HEK293T/(Standard_BC1$HEK293T)) %>%
mutate(iPSC_Fold_Change_Over_Standard = iPSC/(Standard_BC1$iPSC))
Standard_BC2 <- Standard %>%
filter(BC_Pool == 2)
BB_Above_Standard_BC2 <- BB_Above_Standard %>%
filter(BC_Pool == 2) %>%
mutate(K562_Fold_Change_Over_Standard = K562/(Standard_BC2$K562)) %>%
mutate(HEK293T_Fold_Change_Over_Standard = HEK293T/(Standard_BC2$HEK293T)) %>%
mutate(iPSC_Fold_Change_Over_Standard = iPSC/(Standard_BC2$iPSC))
BB_Above_Standard <- rbind(BB_Above_Standard_BC1, BB_Above_Standard_BC2)
##Pivot columns longer for plotting
BB_Above_Standard <- BB_Above_Standard %>%
pivot_longer(K562_Fold_Change_Over_Standard:iPSC_Fold_Change_Over_Standard, names_to = "Cell_Type", values_to = "Fold_Change_Over_Standard")
##Add mean
BB_Above_Standard <- BB_Above_Standard %>%
group_by(Oligo_Number) %>%
mutate(Grand_Mean_Fold_Change = mean(Fold_Change_Over_Standard))
##Plotting
ggplot(BB_Above_Standard, aes(x = log2(Fold_Change_Over_Standard), y = fct_reorder(Oligo_Number, Fold_Change_Over_Standard), fill = Oligo_Number)) +
geom_boxplot(colour = "black", width = 0.35, lwd = 0.6, outlier.shape = NA) +
scale_shape_manual(values = c(16, 16)) +
geom_jitter(position = position_jitterdodge(jitter.width = 0, jitter.height = 0), colour = "black", size = 2.5) +
scale_fill_manual(values=c("black", "#56B4E9", "#56B4E9", "#56B4E9", "#56B4E9", "#56B4E9", "#56B4E9")) +
theme_classic() +
scale_x_continuous(position = "top") +
theme(axis.line = element_line(colour = 'black', size = 0.7)) +
theme(axis.ticks = element_line(colour = "black", size = 0.7)) +
theme(axis.ticks.length=unit(.2, "cm")) +
labs(title = "", x = "", y = "") +
theme(legend.position = "none") +
theme(text = element_text(family="Arial", colour = "black", size = 33))
ggsave("BB_Top_Part_Boxplot.jpeg", width = 6, height = 12, path = "/Users/troymcdiarmid/Documents/U6_pro_series/Figs/Pub_Figs/")
```