From 128ab255b67265f6bd2a704414719b043298e2f0 Mon Sep 17 00:00:00 2001
From: ottiP <ottavia.prunas@edu.unito.it>
Date: Wed, 19 Jan 2022 14:47:50 -0500
Subject: [PATCH] plotting sensitivity analyses

---
 .../plotting_sensitivity_analyses_1.R         | 86 +++++++++++++++++++
 .../plotting_sensitivity_analyses_2.R         | 85 ++++++++++++++++++
 2 files changed, 171 insertions(+)
 create mode 100644 create_figures_ms/plotting_sensitivity_analyses_1.R
 create mode 100644 create_figures_ms/plotting_sensitivity_analyses_2.R

diff --git a/create_figures_ms/plotting_sensitivity_analyses_1.R b/create_figures_ms/plotting_sensitivity_analyses_1.R
new file mode 100644
index 0000000..e66a197
--- /dev/null
+++ b/create_figures_ms/plotting_sensitivity_analyses_1.R
@@ -0,0 +1,86 @@
+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)
+}
+
diff --git a/create_figures_ms/plotting_sensitivity_analyses_2.R b/create_figures_ms/plotting_sensitivity_analyses_2.R
new file mode 100644
index 0000000..b6f30a4
--- /dev/null
+++ b/create_figures_ms/plotting_sensitivity_analyses_2.R
@@ -0,0 +1,85 @@
+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)
+}
\ No newline at end of file