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plotting sensitivity analyses
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ottiP committed Jan 19, 2022
1 parent 480e29b commit 128ab25
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86 changes: 86 additions & 0 deletions create_figures_ms/plotting_sensitivity_analyses_1.R
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plot_VE <- function(v1,v2,v3,v1_post,v2_post,v3_post,x1,x2){
p <- list()

p[[1]] <- ggplot(v1, aes(x=factor(index), y=estimate)) +
geom_point(color=c("blue","black","black"))+
labs(tag = "A") +
theme(plot.tag.position = c(5, 0.01))+
# geom_text(x=0.05, y=100, label="A") +
geom_errorbar(aes(ymin=low, ymax=up), width=0.0,color=c("blue","black","black"))+
coord_cartesian(ylim=c(x1,x2))+
theme_classic() +
xlab('') +
ylab('') +scale_x_discrete(labels=c("1" = "0d", "2" = "1.5d","3"="3d","4"="4.5d"))+
theme(axis.line.x=element_line(color="black"))+
ggtitle("Partially vaccinated \n pre Delta")+
theme(plot.title = element_text(size = 12))

p[[2]] <- ggplot(v2, aes(x=factor(index), y=estimate)) +
geom_point(color=c("blue","black","black"))+
labs(tag = "B") +
theme(plot.tag.position = c(1, 0.02))+
geom_errorbar(aes(ymin=low, ymax=up), width=0.0,color=c("blue","black","black"))+
coord_cartesian(ylim=c(x1,x2))+
theme_classic() +
xlab('') +
ylab('') +scale_x_discrete(labels=c("1" = "main", "2" = "sens1","3"="sens2"))+
theme(axis.line.x=element_line(color="black"))+
ggtitle("Fully vaccinated \n (10-<90d after dose2) pre Delta")+
theme(plot.title = element_text(size = 12))

p[[3]] <- ggplot(v3, aes(x=factor(index), y=estimate)) +
geom_point(color=c("blue","black","black"))+
labs(tag = "C") +
theme(plot.tag.position = c(1, 0.02))+
geom_errorbar(aes(ymin=low, ymax=up), width=0.0,color=c("blue","black","black"))+
coord_cartesian(ylim=c(x1,x2))+
theme_classic() +
xlab('') +
ylab('') +scale_x_discrete(labels=c("1" = "main", "2" = "sens1","3"="sens2"))+
theme(axis.line.x=element_line(color="black"))+
ggtitle("Fully vaccinated \n (>=90d after dose2) pre Delta")+
theme(plot.title = element_text(size = 12))

p[[4]] <- ggplot(v1_post, aes(x=factor(index), y=estimate)) +
geom_point(color=c("blue","black","black"))+
labs(tag = "D") +
theme(plot.tag.position = c(1, 0.02))+
geom_errorbar(aes(ymin=low, ymax=up), width=0.0,color=c("blue","black","black"))+
coord_cartesian(ylim=c(x1,x2))+
theme_classic() +
xlab('') +
ylab('') +scale_x_discrete(labels=c("1" = "main", "2" = "sens1","3"="sens2"))+
theme(axis.line.x=element_line(color="black"))+
ggtitle("Partially vaccinated \n post Delta")+
theme(plot.title = element_text(size = 12))

p[[5]] <- ggplot(v2_post, aes(x=factor(index), y=estimate)) +
geom_point(color=c("blue","black","black"))+
labs(tag = "E") +
theme(plot.tag.position = c(1, 0.02))+
geom_errorbar(aes(ymin=low, ymax=up), width=0.0,color=c("blue","black","black"))+
coord_cartesian(ylim=c(x1,x2))+
theme_classic() +
xlab('') +
ylab('') +scale_x_discrete(labels=c("1" = "main", "2" = "sens1","3"="sens2"))+
theme(axis.line.x=element_line(color="black"))+
ggtitle("Fully vaccinated \n (10-<90d after dose2) post Delta")+
theme(plot.title = element_text(size = 12))

p[[6]] <- ggplot(v3_post, aes(x=factor(index), y=estimate)) +
geom_point(color=c("blue","black","black"))+
labs(tag = "F") +
theme(plot.tag.position = c(1, 0.02))+
geom_errorbar(aes(ymin=low, ymax=up), width=0.0,color=c("blue","black","black"))+
coord_cartesian(ylim=c(x1,x2))+
theme_classic() +
xlab('') +
ylab('') +scale_x_discrete(labels=c("1" = "main", "2" = "sens1","3"="sens2"))+
theme(axis.line.x=element_line(color="black"))+
ggtitle("Fully vaccinated \n (>=90d after dose2) post Delta")+
theme(plot.title = element_text(size = 12))


return(p)
}

85 changes: 85 additions & 0 deletions create_figures_ms/plotting_sensitivity_analyses_2.R
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plot_VE <- function(v1,v2,v3,v1_post,v2_post,v3_post,x1,x2){
p <- list()

p[[1]] <- ggplot(v1, aes(x=factor(index), y=estimate)) +
geom_point(color=c("black","blue","black","black"))+
labs(tag = "A") +
theme(plot.tag.position = c(5, 0.01))+
# geom_text(x=0.05, y=100, label="A") +
geom_errorbar(aes(ymin=low, ymax=up), width=0.0,color=c("black","blue","black","black"))+
coord_cartesian(ylim=c(x1,x2))+
theme_classic() +
xlab('') +
ylab('') +scale_x_discrete(labels=c("1" = "0d", "2" = "1.5d","3"="3d","4"="4.5d"))+
theme(axis.line.x=element_line(color="black"))+
ggtitle("Partially vaccinated \n pre Delta")+
theme(plot.title = element_text(size = 12))

p[[2]] <- ggplot(v2, aes(x=factor(index), y=estimate)) +
geom_point(color=c("black","blue","black","black"))+
labs(tag = "B") +
theme(plot.tag.position = c(1, 0.02))+
geom_errorbar(aes(ymin=low, ymax=up), width=0.0,color=c("black","blue","black","black"))+
coord_cartesian(ylim=c(x1,x2))+
theme_classic() +
xlab('') +
ylab('') +scale_x_discrete(labels=c("1" = "0d", "2" = "1.5d","3"="3d","4"="4.5d"))+
theme(axis.line.x=element_line(color="black"))+
ggtitle("Fully vaccinated \n (10-<90d after dose2) pre Delta")+
theme(plot.title = element_text(size = 12))

p[[3]] <- ggplot(v3, aes(x=factor(index), y=estimate)) +
geom_point(color=c("black","blue","black","black"))+
labs(tag = "C") +
theme(plot.tag.position = c(1, 0.02))+
geom_errorbar(aes(ymin=low, ymax=up), width=0.0,color=c("black","blue","black","black"))+
coord_cartesian(ylim=c(-350,x2))+
theme_classic() +
xlab('') +
ylab('') +scale_x_discrete(labels=c("1" = "0d", "2" = "1.5d","3"="3d","4"="4.5d"))+
theme(axis.line.x=element_line(color="black"))+
ggtitle("Fully vaccinated \n (>=90d after dose2) pre Delta")+
theme(plot.title = element_text(size = 12))

p[[4]] <- ggplot(v1_post, aes(x=factor(index), y=estimate)) +
geom_point(color=c("black","blue","black","black"))+
labs(tag = "D") +
theme(plot.tag.position = c(1, 0.02))+
geom_errorbar(aes(ymin=low, ymax=up), width=0.0,color=c("black","blue","black","black"))+
coord_cartesian(ylim=c(x1,x2))+
theme_classic() +
xlab('') +
ylab('') +scale_x_discrete(labels=c("1" = "0d", "2" = "1.5d","3"="3d","4"="4.5d"))+
theme(axis.line.x=element_line(color="black"))+
ggtitle("Partially vaccinated \n post Delta")+
theme(plot.title = element_text(size = 12))

p[[5]] <- ggplot(v2_post, aes(x=factor(index), y=estimate)) +
geom_point(color=c("black","blue","black","black"))+
labs(tag = "E") +
theme(plot.tag.position = c(1, 0.02))+
geom_errorbar(aes(ymin=low, ymax=up), width=0.0,color=c("black","blue","black","black"))+
coord_cartesian(ylim=c(-350,x2))+
theme_classic() +
xlab('') +
ylab('') +scale_x_discrete(labels=c("1" = "0d", "2" = "1.5d","3"="3d","4"="4.5d"))+
theme(axis.line.x=element_line(color="black"))+
ggtitle("Fully vaccinated \n (10-<90d after dose2) post Delta")+
theme(plot.title = element_text(size = 12))

p[[6]] <- ggplot(v3_post, aes(x=factor(index), y=estimate)) +
geom_point(color=c("black","blue","black","black"))+
labs(tag = "F") +
theme(plot.tag.position = c(1, 0.02))+
geom_errorbar(aes(ymin=low, ymax=up), width=0.0,color=c("black","blue","black","black"))+
coord_cartesian(ylim=c(x1,x2))+
theme_classic() +
xlab('') +
ylab('') +scale_x_discrete(labels=c("1" = "0d", "2" = "1.5d","3"="3d","4"="4.5d"))+
theme(axis.line.x=element_line(color="black"))+
ggtitle("Fully vaccinated \n (>=90d after dose2) post Delta")+
theme(plot.title = element_text(size = 12))


return(p)
}

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