--- a
+++ b/6-Figure scripts/Fig E3.r
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+library(readxl)
+library(ggplot2)
+library(ggrepel)
+
+excel_sheets("Fig E3 Source Data.xlsx")
+
+# Figure E3a ------------------
+dat <- read_excel("Fig E3 Source Data.xlsx", sheet = "Metabolome")
+
+FigE3a.metab <- ggplot(dat) +
+  geom_point(aes(x=NEU, y=EOS), size=2)+
+  theme_bw()+ theme(panel.grid = element_blank()) +
+  geom_hline(yintercept = 0, linetype="twodash") +
+  geom_hline(yintercept = 1, linetype="dashed") +
+  geom_hline(yintercept = -1, linetype="dashed") +
+  geom_vline(xintercept = -1, linetype="dashed") +
+  geom_vline(xintercept = 0, linetype="twodash") +
+  geom_vline(xintercept = 1, linetype="dashed") +
+  xlab("Correlation NEU: Directionality x - log(P)")+
+  ylab("Correlation EOS: Directionality x - log(P)")+
+  ggtitle("Differential MetaB modules")
+FigE3a.metab
+
+
+# Figure E3b ------------------
+dat <- read_excel("Fig E3 Source Data.xlsx", sheet = "Transcriptome")
+
+FigE3b.hostT <- ggplot(dat) +
+  geom_point(aes(x=NEU, y=EOS), size=2)+
+  theme_bw()+ theme(panel.grid = element_blank()) +
+  geom_hline(yintercept = 0, linetype="twodash") +
+  geom_hline(yintercept = 1, linetype="dashed") +
+  geom_hline(yintercept = -1, linetype="dashed") +
+  geom_vline(xintercept = -1, linetype="dashed") +
+  geom_vline(xintercept = 0, linetype="twodash") +
+  geom_vline(xintercept = 1, linetype="dashed") +
+  xlab("Correlation NEU: Directionality x - log(P)")+
+  ylab("Correlation EOS: Directionality x - log(P)")+
+  ggtitle("Differential HostT modules")
+FigE3b.hostT
+
+
+# Figure E3c ------------------
+dat <- read_excel("Fig E3 Source Data.xlsx", sheet = "Sputum Proteome")
+colnames(dat)[1] <- "Label"
+
+FigE3c.sputum <- ggplot(dat) +
+  geom_point(aes(x=NEU, y=EOS), size=2)+
+  geom_text_repel(aes(x=NEU,y=EOS, label = Label),size=3) +
+  theme_bw()+ theme(panel.grid = element_blank()) +
+  geom_hline(yintercept = 0, linetype="twodash") +
+  geom_hline(yintercept = 1, linetype="dashed") +
+  geom_hline(yintercept = -1, linetype="dashed") +
+  geom_vline(xintercept = -1, linetype="dashed") +
+  geom_vline(xintercept = 0, linetype="twodash") +
+  geom_vline(xintercept = 1, linetype="dashed") +
+  xlab("Correlation NEU: Directionality x - log(P)")+
+  ylab("Correlation EOS: Directionality x - log(P)")+
+  ggtitle("Differential sputum proteins")
+FigE3c.sputum
+
+
+# Figure E3d ------------------
+dat <- read_excel("Fig E3 Source Data.xlsx", sheet = "Serum Proteome")
+colnames(dat)[1] <- "Label"
+
+FigE3d.serum <- ggplot(dat) +
+  geom_point(aes(x=NEU2, y=EOS), size=2)+
+  geom_text_repel(aes(x=NEU2,y=EOS, label = Label),size=3) +
+  theme_bw()+ theme(panel.grid = element_blank()) +
+  # geom_hline(yintercept = 0, linetype="twodash") +
+  geom_hline(yintercept = 1, linetype="dashed") +
+  geom_hline(yintercept = -1, linetype="dashed") +
+  geom_vline(xintercept = -1, linetype="dashed") +
+  # geom_vline(xintercept = 0, linetype="twodash") +
+  geom_vline(xintercept = 1, linetype="dashed") +
+  xlab("Correlation NEU: Directionality x - log(P)")+
+  ylab("Correlation EOS: Directionality x - log(P)")+
+  ggtitle("Differential serum proteins")
+FigE3d.serum
+
+# integrate Figures
+library(ggpubr)
+
+FigE3 <- ggarrange(FigE3a.metab, FigE3b.hostT, FigE3c.sputum, FigE3d.serum)
+