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Met_V2.Rmd
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---
title: "Met DMS analysis"
output: html_notebook
code by: Christian Macdonald
---
```{r}
library(ggplot2)
library(gglorenz)
library(readr)
library(stringr)
library(tidyverse)
library(dplyr)
library(ggridges)
library(ggbraid)
library(tidyquant)
library(bio3d)
source("dms_analysis_utilities.R")
library(scales)
library(colorspace)
library(ggpubr)
library(rstatix)
library(cowplot)
```
Read in the Met DMS output
```{r}
# Met Enrich2 score files
met_scores_file = "../data/Enrich2/Met/tsv/TPR_MET_enrich2_config_exp/main_identifiers_scores.tsv"
met_variantscore_colnames <- c("hgvs", "IL3_SE", "IL3_epsilon", "IL3_score",
"IL3_withdrawal_SE", "IL3_withdrawal_epsilon", "IL3_withdrawal_score")
met_variantscore_coltypes <- c("character", "numeric", "numeric", "numeric", "numeric", "numeric", "numeric")
met_scores <- read_delim(met_scores_file, col_names = met_variantscore_colnames, skip=3)
met_scores <- process_hgvs_df(met_scores)
met_scores$is.wt = met_scores$mutation_type == "S"
met_wt_fasta = "Met_wt.fasta"
met_wt_fasta_con=file(met_wt_fasta, open="r")
met_wt_sequence = readLines(met_wt_fasta_con)[2]
close(met_wt_fasta_con)
# Adjust position to correspond with actual numbering
met_scores <- met_scores %>% mutate(pos = pos+1058)
#filters out stops from summarizing
met_avg_scores <- met_scores %>% filter(mutation_type != "N" & mutation_type != "S") %>% group_by(pos) %>% summarise(avg_IL3 = mean(IL3_score, na.rm=TRUE),avg_IL3_withdrawal = mean(IL3_withdrawal_score, na.rm=TRUE))
met_var_scores <- met_scores %>% filter(mutation_type != "N" & mutation_type != "S") %>% group_by(pos) %>% summarise(var_IL3 = var(IL3_score, na.rm=TRUE),var_IL3_withdrawal = var(IL3_withdrawal_score, na.rm=TRUE))
met_max_scores <- met_scores %>% filter(mutation_type != "N" & mutation_type != "S") %>%group_by(pos) %>% summarise(max_IL3 = max(IL3_score, na.rm=TRUE),max_IL3_withdrawal = max(IL3_withdrawal_score, na.rm=TRUE))
```
Read in exon14 Met data
```{r}
# Met Enrich2 score files
ex14_scores_file = "../data/Enrich2/Ex14/tsv/TPR_MET_enrich2_ex_config_exp/main_identifiers_scores.tsv"
met_variantscore_colnames <- c("hgvs", "IL3_SE", "IL3_epsilon", "IL3_score",
"IL3_withdrawal_SE", "IL3_withdrawal_epsilon", "IL3_withdrawal_score")
met_variantscore_coltypes <- c("character", "numeric", "numeric", "numeric", "numeric", "numeric", "numeric")
ex14_scores <- read_delim(ex14_scores_file, col_names = met_variantscore_colnames, skip=3)
ex14_scores <- process_hgvs_df(ex14_scores)
ex14_scores$is.wt = ex14_scores$mutation_type == "S"
met_wt_fasta = "Met_wt.fasta"
met_wt_fasta_con=file(met_wt_fasta, open="r")
met_wt_sequence = readLines(met_wt_fasta_con)[2]
close(met_wt_fasta_con)
# Adjust position to correspond with actual numbering
ex14_scores <- ex14_scores %>% mutate(pos = pos+1058)
ex14_avg_scores <- ex14_scores %>% filter(mutation_type != "N" & mutation_type != "S") %>%group_by(pos) %>% summarise(avg_IL3 = mean(IL3_score, na.rm=TRUE),avg_IL3_withdrawal = mean(IL3_withdrawal_score, na.rm=TRUE))
ex14_var_scores <- ex14_scores %>% filter(mutation_type != "N" & mutation_type != "S") %>% group_by(pos) %>% summarise(var_IL3 = var(IL3_score, na.rm=TRUE),var_IL3_withdrawal = var(IL3_withdrawal_score, na.rm=TRUE))
ex14_max_scores <- ex14_scores %>% filter(mutation_type != "N" & mutation_type != "S") %>% group_by(pos) %>% summarise(max_IL3 = max(IL3_score, na.rm=TRUE),max_IL3_withdrawal = max(IL3_withdrawal_score, na.rm=TRUE))
```
Plot heatmap - IL3 scores
```{r}
order <- c('X','H', 'K', 'R', 'D', 'E',
'C','M','N','Q','S','T','A','I','L','V','W','F',
'Y','G','P')
variant_names <- c('Stop','H', 'K', 'R', 'D', 'E',
'C','M','N','Q','S','T','A','I','L','V','W','F',
'Y','G','P')
met_wt_1 = str_split(substr(met_wt_sequence, 1, 100), '')[[1]]
met_wt_2 = str_split(substr(met_wt_sequence, 101, 200), '')[[1]]
met_wt_3 = str_split(substr(met_wt_sequence, 201, 287), '')[[1]]
Met_row1 = ggplot(data = met_scores %>% filter(pos %in% c(1059:1158)),
aes(x = pos, y = factor(variants, level = order, labels = variant_names), fill = IL3_score )) +
geom_tile(aes(color = as.factor(is.wt)), size = 0.2) +
scale_fill_continuous_divergingx(palette = 'RdBu', mid = 0,l1=0.2, l3 = 0.2, p1=0.9, p3 = .4, p4 = 0.9,rev=FALSE, na.value = 'lightyellow',limits=c(-10,6)) +
scale_color_manual(values = c(NA,'green')) +
scale_x_continuous(breaks = seq(1059, 1158, by = 5),
expand = c(0,0),
sec.axis = sec_axis(
trans = ~.,
name = "Sequence",
breaks = seq(1059, 1158),
labels = met_wt_1,
guide = derive()
)) +
coord_fixed(ratio = 1) +
theme(
panel.background = element_rect(fill = "white",
colour = "white",
size = 0.5, linetype = "solid"),
panel.grid.major = element_line(size = 0.5, linetype = 'solid',
colour = "lightgray"),
panel.grid.minor = element_blank(),
axis.text.x = element_text(angle = 90, hjust = 1, size = 6),
axis.text.y = element_text(size = 4),
axis.text = element_text(size = 4),
axis.text.x.top = element_text(angle = 0, hjust = 0.5, family = "mono"),
axis.ticks = element_blank(),
legend.position="none"
) +
labs(y = "Mutation", x = "Position")
Met_row2 = ggplot(data = met_scores %>% filter(pos %in% c(1159:1258)),
aes(x = pos, y = factor(variants, level = order, labels = variant_names), fill = IL3_score )) +
geom_tile(aes(color = as.factor(is.wt)), size = 0.2) +
scale_fill_continuous_divergingx(palette = 'RdBu', mid = 0,l1=0.2, l3 = 0.2, p1=0.9, p3 = .4, p4 = 0.9,rev=FALSE, na.value = 'lightyellow',limits=c(-10,6)) +
scale_color_manual(values = c(NA,'green')) +
scale_x_continuous(breaks = seq(1159, 1258, by = 5),
expand = c(0,0),
sec.axis = sec_axis(
trans = ~.,
name = "Sequence",
breaks = seq(1159, 1258),
labels = met_wt_2,
guide = derive()
)) +
coord_fixed(ratio = 1) +
theme(
panel.background = element_rect(fill = "white",
colour = "white",
size = 0.5, linetype = "solid"),
panel.grid.major = element_line(size = 0.5, linetype = 'solid',
colour = "lightgray"),
panel.grid.minor = element_blank(),
axis.text.x = element_text(angle = 90, hjust = 1, size = 6),
axis.text.y = element_text(size = 4),
axis.text = element_text(size = 4),
axis.text.x.top = element_text(angle = 0, hjust = 0.5, family = "mono"),
axis.ticks = element_blank(),
legend.position="none"
) +
labs(y = "Mutation", x = "Position")
Met_row3 = ggplot(data = met_scores %>% filter(pos %in% c(1259:1345)),
aes(x = pos, y = factor(variants, level = order, labels = variant_names), fill = IL3_score )) +
geom_tile(aes(color = as.factor(is.wt)), size = 0.2) +
scale_fill_continuous_divergingx(palette = 'RdBu', mid = 0,l1=0.2, l3 = 0.2, p1=0.9, p3 = .4, p4 = 0.9,rev=FALSE, na.value = 'lightyellow',limits=c(-10,6)) +
scale_color_manual(values = c(NA,'green')) +
scale_x_continuous(breaks = seq(1259,1345, by = 5),
expand = c(0,0),
sec.axis = sec_axis(
trans = ~.,
name = "Sequence",
breaks = seq(1259,1345),
labels = met_wt_3,
guide = derive()
)) +
coord_fixed(ratio = 1) +
theme(
panel.background = element_rect(fill = "white",
colour = "white",
size = 0.5, linetype = "solid"),
panel.grid.major = element_line(size = 0.5, linetype = 'solid',
colour = "lightgray"),
panel.grid.minor = element_blank(),
axis.text.x = element_text(angle = 90, hjust = 1, size = 6),
axis.text.y = element_text(size = 4),
axis.text = element_text(size = 4),
axis.text.x.top = element_text(angle = 0, hjust = 0.5, family = "mono"),
axis.ticks = element_blank(),
legend.position="none"
) +
labs(y = "Mutation", x = "Position")
Met_DMS = ggarrange(Met_row1, Met_row2, Met_row3,
nrow = 3, ncol = 1)
ggsave("Plots/Heatmap_IL3_Met.pdf", height = 7, width = 8.5, Met_DMS)
ggsave("Plots/Heatmap_IL3_Met.png", height = 7, width = 8.5, Met_DMS)
```
Plot IL3 withdrawal
```{r}
order <- c('X','H', 'K', 'R', 'D', 'E',
'C','M','N','Q','S','T','A','I','L','V','W','F',
'Y','G','P')
variant_names <- c('Stop','H', 'K', 'R', 'D', 'E',
'C','M','N','Q','S','T','A','I','L','V','W','F',
'Y','G','P')
met_wt_1 = str_split(substr(met_wt_sequence, 1, 100), '')[[1]]
met_wt_2 = str_split(substr(met_wt_sequence, 101, 200), '')[[1]]
met_wt_3 = str_split(substr(met_wt_sequence, 201, 287), '')[[1]]
Met_row1 = ggplot(data = met_scores %>%filter(pos %in% c(1059:1158)),
aes(x = pos, y = factor(variants, level = order, labels = variant_names), fill = IL3_withdrawal_score )) +
geom_tile(aes(color = as.factor(is.wt)), size = 0.2) +
scale_fill_continuous_divergingx(palette = 'RdBu', mid = 0,l1=0.2, l3 = 0.2, p1=0.9, p3 = .4, p4 = 0.9,rev=FALSE, na.value = 'lightyellow',limits=c(-10,6)) +
scale_color_manual(values = c(NA,'green')) +
scale_x_continuous(breaks = seq(1059, 1158, by = 5),
expand = c(0,0),
sec.axis = sec_axis(
trans = ~.,
name = "Sequence",
breaks = seq(1059, 1158),
labels = met_wt_1,
guide = derive()
)) +
coord_fixed(ratio = 1) +
theme(
panel.background = element_rect(fill = "white",
colour = "white",
size = 0.5, linetype = "solid"),
panel.grid.major = element_line(size = 0.5, linetype = 'solid',
colour = "lightgray"),
panel.grid.minor = element_blank(),
axis.text.x = element_text(angle = 90, hjust = 1, size = 6),
axis.text.y = element_text(size = 4),
axis.text = element_text(size = 4),
axis.text.x.top = element_text(angle = 0, hjust = 0.5, family = "mono"),
axis.ticks = element_blank(),
legend.position="none"
) +
labs(y = "Mutation", x = "Position")
Met_row2 = ggplot(data = met_scores %>% filter(pos %in% c(1159:1258)),
aes(x = pos, y = factor(variants, level = order, labels = variant_names), fill = IL3_withdrawal_score )) +
geom_tile(aes(color = as.factor(is.wt)), size = 0.2) +
scale_fill_continuous_divergingx(palette = 'RdBu', mid = 0,l1=0.2, l3 = 0.2, p1=0.9, p3 = .4, p4 = 0.9,rev=FALSE, na.value = 'lightyellow',limits=c(-10,6)) +
scale_color_manual(values = c(NA,'green')) +
scale_x_continuous(breaks = seq(1159, 1258, by = 5),
expand = c(0,0),
sec.axis = sec_axis(
trans = ~.,
name = "Sequence",
breaks = seq(1159, 1258),
labels = met_wt_2,
guide = derive()
)) +
coord_fixed(ratio = 1) +
theme(
panel.background = element_rect(fill = "white",
colour = "white",
size = 0.5, linetype = "solid"),
panel.grid.major = element_line(size = 0.5, linetype = 'solid',
colour = "lightgray"),
panel.grid.minor = element_blank(),
axis.text.x = element_text(angle = 90, hjust = 1, size = 6),
axis.text.y = element_text(size = 4),
axis.text = element_text(size = 4),
axis.text.x.top = element_text(angle = 0, hjust = 0.5, family = "mono"),
axis.ticks = element_blank(),
legend.position="none"
) +
labs(y = "Mutation", x = "Position")
Met_row3 = ggplot(data = met_scores %>% filter(pos %in% c(1259:1345)),
aes(x = pos, y = factor(variants, level = order, labels = variant_names), fill = IL3_withdrawal_score )) +
geom_tile(aes(color = as.factor(is.wt)), size = 0.2) +
scale_fill_continuous_divergingx(palette = 'RdBu', mid = 0,l1=0.2, l3 = 0.2, p1=0.9, p3 = .4, p4 = 0.9,rev=FALSE, na.value = 'lightyellow',limits=c(-10,6)) +
scale_color_manual(values = c(NA,'green')) +
scale_x_continuous(breaks = seq(1259,1345, by = 5),
expand = c(0,0),
sec.axis = sec_axis(
trans = ~.,
name = "Sequence",
breaks = seq(1259,1345),
labels = met_wt_3,
guide = derive()
)) +
coord_fixed(ratio = 1) +
theme(
panel.background = element_rect(fill = "white",
colour = "white",
size = 0.5, linetype = "solid"),
panel.grid.major = element_line(size = 0.5, linetype = 'solid',
colour = "lightgray"),
panel.grid.minor = element_blank(),
axis.text.x = element_text(angle = 90, hjust = 1, size = 6),
axis.text.y = element_text(size = 4),
axis.text = element_text(size = 4),
axis.text.x.top = element_text(angle = 0, hjust = 0.5, family = "mono"),
axis.ticks = element_blank(),
legend.position="right"
) +
labs(y = "Mutation", x = "Position")
Met_DMS = ggarrange(Met_row1, Met_row2, Met_row3,
nrow = 3, ncol = 1)
ggsave("Plots/Heatmap_IL3_withdrawal_Met.pdf", height = 7, width = 8.5, Met_DMS)
ggsave("Plots/Heatmap_IL3_withdrawal_Met.png", height = 7, width = 8.5, Met_DMS)
######################### 2 row
order <- c('X','H', 'K', 'R', 'D', 'E',
'C','M','N','Q','S','T','A','I','L','V','W','F',
'Y','G','P')
variant_names <- c('Stop','H', 'K', 'R', 'D', 'E',
'C','M','N','Q','S','T','A','I','L','V','W','F',
'Y','G','P')
met_wt_1 = str_split(substr(met_wt_sequence, 1, 144), '')[[1]]
met_wt_2 = str_split(substr(met_wt_sequence, 145, 287), '')[[1]]
Met_row1 = ggplot(data = met_scores %>%filter(pos %in% c(1059:1202)),
aes(x = pos, y = factor(variants, level = order, labels = variant_names), fill = IL3_withdrawal_score )) +
geom_tile(aes(color = as.factor(is.wt)), size = 0.2) +
scale_fill_continuous_divergingx(palette = 'RdBu', mid = 0,l1=0.2, l3 = 0.2, p1=0.9, p3 = .4, p4 = 0.9,rev=FALSE, na.value = 'lightyellow',limits=c(-10,6)) +
scale_color_manual(values = c(NA,'green')) +
scale_x_continuous(breaks = seq(1059,1202, by = 5),
expand = c(0,0),
sec.axis = sec_axis(
trans = ~.,
name = "Sequence",
breaks = seq(1059,1202),
labels = met_wt_1,
guide = derive()
)) +
coord_fixed(ratio = 1) +
theme(
panel.background = element_rect(fill = "white",
colour = "white",
size = 0.5, linetype = "solid"),
panel.grid.major = element_line(size = 0.5, linetype = 'solid',
colour = "lightgray"),
panel.grid.minor = element_blank(),
axis.text.x = element_text(angle = 90, hjust = 1, size = 6),
axis.text.y = element_text(size = 4),
axis.text = element_text(size = 4),
axis.text.x.top = element_text(angle = 0, hjust = 0.5, family = "mono"),
axis.ticks = element_blank(),
legend.position="none"
) +
labs(y = "Mutation", x = "Position")
Met_row2 = ggplot(data = met_scores %>% filter(pos %in% c(1203:1345)),
aes(x = pos, y = factor(variants, level = order, labels = variant_names), fill = IL3_withdrawal_score )) +
geom_tile(aes(color = as.factor(is.wt)), size = 0.2) +
scale_fill_continuous_divergingx(palette = 'RdBu', mid = 0,l1=0.2, l3 = 0.2, p1=0.9, p3 = .4, p4 = 0.9,rev=FALSE, na.value = 'lightyellow',limits=c(-10,6)) +
scale_color_manual(values = c(NA,'green')) +
scale_x_continuous(breaks = seq(1203,1345, by = 5),
expand = c(0,0),
sec.axis = sec_axis(
trans = ~.,
name = "Sequence",
breaks = seq(1203,1345),
labels = met_wt_2,
guide = derive()
)) +
coord_fixed(ratio = 1) +
theme(
panel.background = element_rect(fill = "white",
colour = "white",
size = 0.5, linetype = "solid"),
panel.grid.major = element_line(size = 0.5, linetype = 'solid',
colour = "lightgray"),
panel.grid.minor = element_blank(),
axis.text.x = element_text(angle = 90, hjust = 1, size = 6),
axis.text.y = element_text(size = 4),
axis.text = element_text(size = 4),
axis.text.x.top = element_text(angle = 0, hjust = 0.5, family = "mono"),
axis.ticks = element_blank(),
legend.position="none"
) +
labs(y = "Mutation", x = "Position")
Met_DMS = ggarrange(Met_row1,Met_row2,nrow = 2, ncol = 1)
ggsave("Plots/Heatmap_IL3_withdrawal_Met_2.pdf", height = 7, width = 8.5, Met_DMS)
ggsave("Plots/Heatmap_IL3_withdrawal_Met_2.pdf", height = 7, width = 8.5, Met_DMS)
######### 2 row
order <- c('X','H', 'K', 'R', 'D', 'E',
'C','M','N','Q','S','T','A','I','L','V','W','F',
'Y','G','P')
variant_names <- c('Stop','H', 'K', 'R', 'D', 'E',
'C','M','N','Q','S','T','A','I','L','V','W','F',
'Y','G','P')
met_wt_1 = str_split(substr(met_wt_sequence, 1, 144), '')[[1]]
met_wt_2 = str_split(substr(met_wt_sequence, 145, 287), '')[[1]]
Met_row1 = ggplot(data = met_scores %>%filter(pos %in% c(1059:1202)),
aes(x = pos, y = factor(variants, level = order, labels = variant_names), fill = IL3_score )) +
geom_tile(aes(color = as.factor(is.wt)), size = 0.2) +
scale_fill_continuous_divergingx(palette = 'RdBu', mid = 0,l1=0.2, l3 = 0.2, p1=0.9, p3 = .4, p4 = 0.9,rev=FALSE, na.value = 'lightyellow',limits=c(-10,6)) +
scale_color_manual(values = c(NA,'green')) +
scale_x_continuous(breaks = seq(1059,1202, by = 5),
expand = c(0,0),
sec.axis = sec_axis(
trans = ~.,
name = "Sequence",
breaks = seq(1059,1202),
labels = met_wt_1,
guide = derive()
)) +
coord_fixed(ratio = 1) +
theme(
panel.background = element_rect(fill = "white",
colour = "white",
size = 0.5, linetype = "solid"),
panel.grid.major = element_line(size = 0.5, linetype = 'solid',
colour = "lightgray"),
panel.grid.minor = element_blank(),
axis.text.x = element_text(angle = 90, hjust = 1, size = 6),
axis.text.y = element_text(size = 4),
axis.text = element_text(size = 4),
axis.text.x.top = element_text(angle = 0, hjust = 0.5, family = "mono"),
axis.ticks = element_blank(),
legend.position="none"
) +
labs(y = "Mutation", x = "Position")
Met_row2 = ggplot(data = met_scores %>% filter(pos %in% c(1203:1345)),
aes(x = pos, y = factor(variants, level = order, labels = variant_names), fill = IL3_score )) +
geom_tile(aes(color = as.factor(is.wt)), size = 0.2) +
scale_fill_continuous_divergingx(palette = 'RdBu', mid = 0,l1=0.2, l3 = 0.2, p1=0.9, p3 = .4, p4 = 0.9,rev=FALSE, na.value = 'lightyellow',limits=c(-10,6)) +
scale_color_manual(values = c(NA,'green')) +
scale_x_continuous(breaks = seq(1203,1345, by = 5),
expand = c(0,0),
sec.axis = sec_axis(
trans = ~.,
name = "Sequence",
breaks = seq(1203,1345),
labels = met_wt_2,
guide = derive()
)) +
coord_fixed(ratio = 1) +
theme(
panel.background = element_rect(fill = "white",
colour = "white",
size = 0.5, linetype = "solid"),
panel.grid.major = element_line(size = 0.5, linetype = 'solid',
colour = "lightgray"),
panel.grid.minor = element_blank(),
axis.text.x = element_text(angle = 90, hjust = 1, size = 6),
axis.text.y = element_text(size = 4),
axis.text = element_text(size = 4),
axis.text.x.top = element_text(angle = 0, hjust = 0.5, family = "mono"),
axis.ticks = element_blank(),
legend.position="none"
) +
labs(y = "Mutation", x = "Position")
Met_DMS = ggarrange(Met_row1,Met_row2,nrow = 2, ncol = 1)
ggsave("Plots/Heatmap_IL3_met_2.pdf", height = 7, width = 8.5, Met_DMS)
ggsave("Plots/Heatmap_IL3_met_2.pdf", height = 7, width = 8.5, Met_DMS)
order <- c('X','H', 'K', 'R', 'D', 'E',
'C','M','N','Q','S','T','A','I','L','V','W','F',
'Y','G','P')
variant_names <- c('Stop','H', 'K', 'R', 'D', 'E',
'C','M','N','Q','S','T','A','I','L','V','W','F',
'Y','G','P')
met_wt_1 = str_split(substr(met_wt_sequence, 1, 144), '')[[1]]
met_wt_2 = str_split(substr(met_wt_sequence, 145, 287), '')[[1]]
Met_row1 = ggplot(data = met_scores %>%filter(pos %in% c(1059:1202)),
aes(x = pos, y = factor(variants, level = order, labels = variant_names), fill = IL3_withdrawal_score )) +
geom_tile(aes(color = as.factor(is.wt)), size = 0.2) +
scale_fill_continuous_divergingx(palette = 'RdBu', mid = 0,l1=0.2, l3 = 0.2, p1=0.9, p3 = .4, p4 = 0.9,rev=FALSE, na.value = 'lightyellow',limits=c(-10,6)) +
scale_color_manual(values = c(NA,'green')) +
scale_x_continuous(breaks = seq(1059,1202, by = 5),
expand = c(0,0),
sec.axis = sec_axis(
trans = ~.,
name = "Sequence",
breaks = seq(1059,1202),
labels = met_wt_1,
guide = derive()
)) +
coord_fixed(ratio = 1) +
theme(
panel.background = element_rect(fill = "white",
colour = "white",
size = 0.5, linetype = "solid"),
panel.grid.major = element_line(size = 0.5, linetype = 'solid',
colour = "lightgray"),
panel.grid.minor = element_blank(),
axis.text.x = element_text(angle = 90, hjust = 1, size = 6),
axis.text.y = element_text(size = 4),
axis.text = element_text(size = 4),
axis.text.x.top = element_text(angle = 0, hjust = 0.5, family = "mono"),
axis.ticks = element_blank(),
legend.position="none"
) +
labs(y = "Mutation", x = "Position")
Met_row2 = ggplot(data = met_scores %>% filter(pos %in% c(1203:1345)),
aes(x = pos, y = factor(variants, level = order, labels = variant_names), fill = IL3_withdrawal_score )) +
geom_tile(aes(color = as.factor(is.wt)), size = 0.2) +
scale_fill_continuous_divergingx(palette = 'RdBu', mid = 0,l1=0.2, l3 = 0.2, p1=0.9, p3 = .4, p4 = 0.9,rev=FALSE, na.value = 'lightyellow',limits=c(-10,6)) +
scale_color_manual(values = c(NA,'green')) +
scale_x_continuous(breaks = seq(1203,1345, by = 5),
expand = c(0,0),
sec.axis = sec_axis(
trans = ~.,
name = "Sequence",
breaks = seq(1203,1345),
labels = met_wt_2,
guide = derive()
)) +
coord_fixed(ratio = 1) +
theme(
panel.background = element_rect(fill = "white",
colour = "white",
size = 0.5, linetype = "solid"),
panel.grid.major = element_line(size = 0.5, linetype = 'solid',
colour = "lightgray"),
panel.grid.minor = element_blank(),
axis.text.x = element_text(angle = 90, hjust = 1, size = 6),
axis.text.y = element_text(size = 4),
axis.text = element_text(size = 4),
axis.text.x.top = element_text(angle = 0, hjust = 0.5, family = "mono"),
axis.ticks = element_blank(),
legend.position="none"
) +
labs(y = "Mutation", x = "Position")
Met_DMS = ggarrange(Met_row1,Met_row2,nrow = 2, ncol = 1)
ggsave("Plots/Heatmap_IL3_withdrawal_met_2.pdf", height = 7, width = 8.5, Met_DMS)
ggsave("Plots/Heatmap_IL3_withdrawal_met_2.pdf", height = 7, width = 8.5, Met_DMS)
```
Exon 14 heatmaps.
Plot heatmap - exon 14, IL3 scores
```{r}
order <- c('X','H', 'K', 'R', 'D', 'E',
'C','M','N','Q','S','T','A','I','L','V','W','F',
'Y','G','P')
variant_names <- c('Stop','H', 'K', 'R', 'D', 'E',
'C','M','N','Q','S','T','A','I','L','V','W','F',
'Y','G','P')
met_wt_1 = str_split(substr(met_wt_sequence, 1, 100), '')[[1]]
met_wt_2 = str_split(substr(met_wt_sequence, 101, 200), '')[[1]]
met_wt_3 = str_split(substr(met_wt_sequence, 201, 287), '')[[1]]
Met_row1 = ggplot(data = ex14_scores %>% filter(pos %in% c(1059:1158)),
aes(x = pos, y = factor(variants, level = order, labels = variant_names), fill = IL3_score )) +
geom_tile(aes(color = as.factor(is.wt)), size = 0.2) +
scale_fill_continuous_divergingx(palette = 'RdBu', mid = 0,l1=0.2, l3 = 0.2, p1=0.9, p3 = .4, p4 = 0.9,rev=FALSE, na.value = 'lightyellow',limits=c(-10,6)) +
scale_color_manual(values = c(NA,'green')) +
scale_x_continuous(breaks = seq(1059, 1158, by = 5),
expand = c(0,0),
sec.axis = sec_axis(
trans = ~.,
name = "Sequence",
breaks = seq(1059, 1158),
labels = met_wt_1,
guide = derive()
)) +
coord_fixed(ratio = 1) +
theme(
panel.background = element_rect(fill = "white",
colour = "white",
size = 0.5, linetype = "solid"),
panel.grid.major = element_line(size = 0.5, linetype = 'solid',
colour = "lightgray"),
panel.grid.minor = element_blank(),
axis.text.x = element_text(angle = 90, hjust = 1, size = 6),
axis.text.y = element_text(size = 4),
axis.text = element_text(size = 4),
axis.text.x.top = element_text(angle = 0, hjust = 0.5, family = "mono"),
axis.ticks = element_blank(),
legend.position="none"
) +
labs(y = "Mutation", x = "Position")
Met_row2 = ggplot(data = ex14_scores %>% filter(pos %in% c(1159:1258)),
aes(x = pos, y = factor(variants, level = order, labels = variant_names), fill = IL3_score )) +
geom_tile(aes(color = as.factor(is.wt)), size = 0.2) +
scale_fill_continuous_divergingx(palette = 'RdBu', mid = 0,l1=0.2, l3 = 0.2, p1=0.9, p3 = .4, p4 = 0.9,rev=FALSE, na.value = 'lightyellow',limits=c(-10,6)) +
scale_color_manual(values = c(NA,'green')) +
scale_x_continuous(breaks = seq(1159, 1258, by = 5),
expand = c(0,0),
sec.axis = sec_axis(
trans = ~.,
name = "Sequence",
breaks = seq(1159, 1258),
labels = met_wt_2,
guide = derive()
)) +
coord_fixed(ratio = 1) +
theme(
panel.background = element_rect(fill = "white",
colour = "white",
size = 0.5, linetype = "solid"),
panel.grid.major = element_line(size = 0.5, linetype = 'solid',
colour = "lightgray"),
panel.grid.minor = element_blank(),
axis.text.x = element_text(angle = 90, hjust = 1, size = 6),
axis.text.y = element_text(size = 4),
axis.text = element_text(size = 4),
axis.text.x.top = element_text(angle = 0, hjust = 0.5, family = "mono"),
axis.ticks = element_blank(),
legend.position="none"
) +
labs(y = "Mutation", x = "Position")
Met_row3 = ggplot(data = ex14_scores %>% filter(pos %in% c(1259:1345)),
aes(x = pos, y = factor(variants, level = order, labels = variant_names), fill = IL3_score )) +
geom_tile(aes(color = as.factor(is.wt)), size = 0.2) +
scale_fill_continuous_divergingx(palette = 'RdBu', mid = 0,l1=0.2, l3 = 0.2, p1=0.9, p3 = .4, p4 = 0.9,rev=FALSE, na.value = 'lightyellow',limits=c(-10,6)) +
scale_color_manual(values = c(NA,'green')) +
scale_x_continuous(breaks = seq(1259,1345, by = 5),
expand = c(0,0),
sec.axis = sec_axis(
trans = ~.,
name = "Sequence",
breaks = seq(1259,1345),
labels = met_wt_3,
guide = derive()
)) +
coord_fixed(ratio = 1) +
theme(
panel.background = element_rect(fill = "white",
colour = "white",
size = 0.5, linetype = "solid"),
panel.grid.major = element_line(size = 0.5, linetype = 'solid',
colour = "lightgray"),
panel.grid.minor = element_blank(),
axis.text.x = element_text(angle = 90, hjust = 1, size = 6),
axis.text.y = element_text(size = 4),
axis.text = element_text(size = 4),
axis.text.x.top = element_text(angle = 0, hjust = 0.5, family = "mono"),
axis.ticks = element_blank(),
legend.position="none"
) +
labs(y = "Mutation", x = "Position")
Met_DMS = ggarrange(Met_row1, Met_row2, Met_row3,
nrow = 3, ncol = 1)
ggsave("Plots/Heatmap_IL3_ex14.pdf", height = 7, width = 8.5, Met_DMS)
ggsave("Plots/Heatmap_IL3_ex14.png", height = 7, width = 8.5, Met_DMS)
######### 2 row
order <- c('X','H', 'K', 'R', 'D', 'E',
'C','M','N','Q','S','T','A','I','L','V','W','F',
'Y','G','P')
variant_names <- c('Stop','H', 'K', 'R', 'D', 'E',
'C','M','N','Q','S','T','A','I','L','V','W','F',
'Y','G','P')
met_wt_1 = str_split(substr(met_wt_sequence, 1, 144), '')[[1]]
met_wt_2 = str_split(substr(met_wt_sequence, 145, 287), '')[[1]]
Met_row1 = ggplot(data = ex14_scores %>%filter(pos %in% c(1059:1202)),
aes(x = pos, y = factor(variants, level = order, labels = variant_names), fill = IL3_score )) +
geom_tile(aes(color = as.factor(is.wt)), size = 0.2) +
scale_fill_continuous_divergingx(palette = 'RdBu', mid = 0,l1=0.2, l3 = 0.2, p1=0.9, p3 = .4, p4 = 0.9,rev=FALSE, na.value = 'lightyellow',limits=c(-10,6)) +
scale_color_manual(values = c(NA,'green')) +
scale_x_continuous(breaks = seq(1059,1202, by = 5),
expand = c(0,0),
sec.axis = sec_axis(
trans = ~.,
name = "Sequence",
breaks = seq(1059,1202),
labels = met_wt_1,
guide = derive()
)) +
coord_fixed(ratio = 1) +
theme(
panel.background = element_rect(fill = "white",
colour = "white",
size = 0.5, linetype = "solid"),
panel.grid.major = element_line(size = 0.5, linetype = 'solid',
colour = "lightgray"),
panel.grid.minor = element_blank(),
axis.text.x = element_text(angle = 90, hjust = 1, size = 6),
axis.text.y = element_text(size = 4),
axis.text = element_text(size = 4),
axis.text.x.top = element_text(angle = 0, hjust = 0.5, family = "mono"),
axis.ticks = element_blank(),
legend.position="none"
) +
labs(y = "Mutation", x = "Position")
Met_row2 = ggplot(data = ex14_scores %>% filter(pos %in% c(1203:1345)),
aes(x = pos, y = factor(variants, level = order, labels = variant_names), fill = IL3_score )) +
geom_tile(aes(color = as.factor(is.wt)), size = 0.2) +
scale_fill_continuous_divergingx(palette = 'RdBu', mid = 0,l1=0.2, l3 = 0.2, p1=0.9, p3 = .4, p4 = 0.9,rev=FALSE, na.value = 'lightyellow',limits=c(-10,6)) +
scale_color_manual(values = c(NA,'green')) +
scale_x_continuous(breaks = seq(1203,1345, by = 5),
expand = c(0,0),
sec.axis = sec_axis(
trans = ~.,
name = "Sequence",
breaks = seq(1203,1345),
labels = met_wt_2,
guide = derive()
)) +
coord_fixed(ratio = 1) +
theme(
panel.background = element_rect(fill = "white",
colour = "white",
size = 0.5, linetype = "solid"),
panel.grid.major = element_line(size = 0.5, linetype = 'solid',
colour = "lightgray"),
panel.grid.minor = element_blank(),
axis.text.x = element_text(angle = 90, hjust = 1, size = 6),
axis.text.y = element_text(size = 4),
axis.text = element_text(size = 4),
axis.text.x.top = element_text(angle = 0, hjust = 0.5, family = "mono"),
axis.ticks = element_blank(),
legend.position="none"
) +
labs(y = "Mutation", x = "Position")
Met_DMS = ggarrange(Met_row1,Met_row2,nrow = 2, ncol = 1)
ggsave("Plots/Heatmap_IL3_ex14_2.pdf", height = 7, width = 8.5, Met_DMS)
ggsave("Plots/Heatmap_IL3_ex14_2.pdf", height = 7, width = 8.5, Met_DMS)
```
Plot IL3 withdrawal, exon 14
```{r}
order <- c('X','H', 'K', 'R', 'D', 'E',
'C','M','N','Q','S','T','A','I','L','V','W','F',
'Y','G','P')
variant_names <- c('Stop','H', 'K', 'R', 'D', 'E',
'C','M','N','Q','S','T','A','I','L','V','W','F',
'Y','G','P')
met_wt_1 = str_split(substr(met_wt_sequence, 1, 100), '')[[1]]
met_wt_2 = str_split(substr(met_wt_sequence, 101, 200), '')[[1]]
met_wt_3 = str_split(substr(met_wt_sequence, 201, 287), '')[[1]]
Met_row1 = ggplot(data = ex14_scores %>% filter(pos %in% c(1059:1158)),
aes(x = pos, y = factor(variants, level = order, labels = variant_names), fill = IL3_withdrawal_score )) +
geom_tile(aes(color = as.factor(is.wt)), size = 0.2) +
scale_fill_continuous_divergingx(palette = 'RdBu', mid = 0,l1=0.2, l3 = 0.2, p1=0.9, p3 = .4, p4 = 0.9,rev=FALSE, na.value = 'lightyellow',limits=c(-10,6)) +
scale_color_manual(values = c(NA,'green')) +
scale_x_continuous(breaks = seq(1059, 1158, by = 5),
expand = c(0,0),
sec.axis = sec_axis(
trans = ~.,
name = "Sequence",
breaks = seq(1059, 1158),
labels = met_wt_1,
guide = derive()
)) +
coord_fixed(ratio = 1) +
theme(
panel.background = element_rect(fill = "white",
colour = "white",
size = 0.5, linetype = "solid"),
panel.grid.major = element_line(size = 0.5, linetype = 'solid',
colour = "lightgray"),
panel.grid.minor = element_blank(),
axis.text.x = element_text(angle = 90, hjust = 1, size = 6),
axis.text.y = element_text(size = 4),
axis.text = element_text(size = 4),
axis.text.x.top = element_text(angle = 0, hjust = 0.5, family = "mono"),
axis.ticks = element_blank(),
legend.position="none"
) +
labs(y = "Mutation", x = "Position")
Met_row2 = ggplot(data = ex14_scores %>% filter(pos %in% c(1159:1258)),
aes(x = pos, y = factor(variants, level = order, labels = variant_names), fill = IL3_withdrawal_score )) +
geom_tile(aes(color = as.factor(is.wt)), size = 0.2) +
scale_fill_continuous_divergingx(palette = 'RdBu', mid = 0,l1=0.2, l3 = 0.2, p1=0.9, p3 = .4, p4 = 0.9,rev=FALSE, na.value = 'lightyellow',limits=c(-10,6)) +
scale_color_manual(values = c(NA,'green')) +
scale_x_continuous(breaks = seq(1159, 1258, by = 5),
expand = c(0,0),
sec.axis = sec_axis(
trans = ~.,
name = "Sequence",
breaks = seq(1159, 1258),
labels = met_wt_2,
guide = derive()
)) +
coord_fixed(ratio = 1) +
theme(
panel.background = element_rect(fill = "white",
colour = "white",
size = 0.5, linetype = "solid"),
panel.grid.major = element_line(size = 0.5, linetype = 'solid',
colour = "lightgray"),
panel.grid.minor = element_blank(),
axis.text.x = element_text(angle = 90, hjust = 1, size = 6),
axis.text.y = element_text(size = 4),
axis.text = element_text(size = 4),
axis.text.x.top = element_text(angle = 0, hjust = 0.5, family = "mono"),
axis.ticks = element_blank(),
legend.position="none"
) +
labs(y = "Mutation", x = "Position")
Met_row3 = ggplot(data = ex14_scores %>% filter(pos %in% c(1259:1345)),
aes(x = pos, y = factor(variants, level = order, labels = variant_names), fill = IL3_withdrawal_score )) +
geom_tile(aes(color = as.factor(is.wt)), size = 0.2) +
scale_fill_continuous_divergingx(palette = 'RdBu', mid = 0,l1=0.2, l3 = 0.2, p1=0.9, p3 = .4, p4 = 0.9,rev=FALSE, na.value = 'lightyellow',limits=c(-10,6)) +
scale_color_manual(values = c(NA,'green')) +
scale_x_continuous(breaks = seq(1259,1345, by = 5),
expand = c(0,0),
sec.axis = sec_axis(
trans = ~.,
name = "Sequence",
breaks = seq(1259,1345),
labels = met_wt_3,
guide = derive()
)) +
coord_fixed(ratio = 1) +
theme(
panel.background = element_rect(fill = "white",
colour = "white",
size = 0.5, linetype = "solid"),
panel.grid.major = element_line(size = 0.5, linetype = 'solid',
colour = "lightgray"),
panel.grid.minor = element_blank(),
axis.text.x = element_text(angle = 90, hjust = 1, size = 6),
axis.text.y = element_text(size = 4),
axis.text = element_text(size = 4),
axis.text.x.top = element_text(angle = 0, hjust = 0.5, family = "mono"),
axis.ticks = element_blank(),
legend.position="right"
) +
labs(y = "Mutation", x = "Position")
Met_DMS = ggarrange(Met_row1, Met_row2, Met_row3,
nrow = 3, ncol = 1)
ggsave("Plots/Heatmap_IL3_withdrawal_ex14.pdf", height = 7, width = 8.5, Met_DMS)
ggsave("Plots/Heatmap_IL3_withdrawal_ex14.png", height = 7, width = 8.5, Met_DMS)
######### 2 row
order <- c('X','H', 'K', 'R', 'D', 'E',
'C','M','N','Q','S','T','A','I','L','V','W','F',
'Y','G','P')
variant_names <- c('Stop','H', 'K', 'R', 'D', 'E',
'C','M','N','Q','S','T','A','I','L','V','W','F',
'Y','G','P')
met_wt_1 = str_split(substr(met_wt_sequence, 1, 144), '')[[1]]
met_wt_2 = str_split(substr(met_wt_sequence, 145, 287), '')[[1]]
Met_row1 = ggplot(data = ex14_scores %>%filter(pos %in% c(1059:1202)),
aes(x = pos, y = factor(variants, level = order, labels = variant_names), fill = IL3_withdrawal_score )) +
geom_tile(aes(color = as.factor(is.wt)), size = 0.2) +
scale_fill_continuous_divergingx(palette = 'RdBu', mid = 0,l1=0.2, l3 = 0.2, p1=0.9, p3 = .4, p4 = 0.9,rev=FALSE, na.value = 'lightyellow',limits=c(-10,6)) +
scale_color_manual(values = c(NA,'green')) +
scale_x_continuous(breaks = seq(1059,1202, by = 5),
expand = c(0,0),
sec.axis = sec_axis(
trans = ~.,
name = "Sequence",
breaks = seq(1059,1202),
labels = met_wt_1,
guide = derive()
)) +
coord_fixed(ratio = 1) +
theme(
panel.background = element_rect(fill = "white",
colour = "white",
size = 0.5, linetype = "solid"),
panel.grid.major = element_line(size = 0.5, linetype = 'solid',
colour = "lightgray"),
panel.grid.minor = element_blank(),
axis.text.x = element_text(angle = 90, hjust = 1, size = 6),
axis.text.y = element_text(size = 4),
axis.text = element_text(size = 4),
axis.text.x.top = element_text(angle = 0, hjust = 0.5, family = "mono"),
axis.ticks = element_blank(),
legend.position="none"
) +
labs(y = "Mutation", x = "Position")
Met_row2 = ggplot(data = ex14_scores %>% filter(pos %in% c(1203:1345)),
aes(x = pos, y = factor(variants, level = order, labels = variant_names), fill = IL3_withdrawal_score )) +
geom_tile(aes(color = as.factor(is.wt)), size = 0.2) +
scale_fill_continuous_divergingx(palette = 'RdBu', mid = 0,l1=0.2, l3 = 0.2, p1=0.9, p3 = .4, p4 = 0.9,rev=FALSE, na.value = 'lightyellow',limits=c(-10,6)) +
scale_color_manual(values = c(NA,'green')) +
scale_x_continuous(breaks = seq(1203,1345, by = 5),
expand = c(0,0),
sec.axis = sec_axis(
trans = ~.,
name = "Sequence",
breaks = seq(1203,1345),
labels = met_wt_2,
guide = derive()
)) +
coord_fixed(ratio = 1) +
theme(
panel.background = element_rect(fill = "white",
colour = "white",
size = 0.5, linetype = "solid"),
panel.grid.major = element_line(size = 0.5, linetype = 'solid',
colour = "lightgray"),
panel.grid.minor = element_blank(),
axis.text.x = element_text(angle = 90, hjust = 1, size = 6),
axis.text.y = element_text(size = 4),
axis.text = element_text(size = 4),
axis.text.x.top = element_text(angle = 0, hjust = 0.5, family = "mono"),
axis.ticks = element_blank(),
legend.position="none"
) +
labs(y = "Mutation", x = "Position")
Met_DMS = ggarrange(Met_row1,Met_row2,nrow = 2, ncol = 1)
ggsave("Plots/Heatmap_IL3_withdrawal_ex14_2.pdf", height = 7, width = 8.5, Met_DMS)
ggsave("Plots/Heatmap_IL3_withdrawal_ex14_2.pdf", height = 7, width = 8.5, Met_DMS)
```{r}
######### 2 row
order <- c('X','H', 'K', 'R', 'D', 'E',
'C','M','N','Q','S','T','A','I','L','V','W','F',
'Y','G','P')
variant_names <- c('Stop','H', 'K', 'R', 'D', 'E',
'C','M','N','Q','S','T','A','I','L','V','W','F',
'Y','G','P')
met_wt_1 = str_split(substr(met_wt_sequence, 1, 144), '')[[1]]
met_wt_2 = str_split(substr(met_wt_sequence, 145, 287), '')[[1]]
Met_row1 = ggplot(data = ex14_scores %>%filter(pos %in% c(1059:1202)),
aes(x = pos, y = factor(variants, level = order, labels = variant_names), fill = IL3_withdrawal_score )) +
geom_tile(aes(color = as.factor(is.wt)), size = 0.2) +
scale_fill_continuous_divergingx(palette = 'RdBu', mid = 0,l1=0.2, l3 = 0.2, p1=0.9, p3 = .4, p4 = 0.9,rev=FALSE, na.value = 'lightyellow',limits=c(-10,6)) +
scale_color_manual(values = c(NA,'green')) +
scale_x_continuous(breaks = seq(1059,1202, by = 5),
expand = c(0,0),
sec.axis = sec_axis(
trans = ~.,
name = "Sequence",
breaks = seq(1059,1202),
labels = met_wt_1,
guide = derive()
)) +
coord_fixed(ratio = 1) +
theme(
panel.background = element_rect(fill = "white",
colour = "white",
size = 0.5, linetype = "solid"),
panel.grid.major = element_line(size = 0.5, linetype = 'solid',