--- a
+++ b/6-Figure scripts/Fig 1.r
@@ -0,0 +1,104 @@
+library(readxl)
+library(dplyr)
+
+# Figure 1a ------------------------------------------
+# Figure 1a. taxonomy #######
+rm(list = ls())
+dat.taxa <- read_excel("Fig 1 Source Data.xlsx", sheet = "Fig 1a taxonomy PCA")
+dat.funct <- read_excel("Fig 1 Source Data.xlsx", sheet = "Fig 1a metagenome PCA")
+
+pca <- dat.taxa
+Fig1a.taxa.pca <- ggplot(pca,aes(PC1,PC2))+
+  geom_point(size=2,aes(col=Disease,shape=Cohort))+ 
+  scale_color_manual(values=c("#f0999f","#46bbc0"))+
+  scale_shape_manual(values=c(16,15)) +
+  theme_bw()+theme(axis.line = element_line(colour = "black"),
+                   panel.grid.major = element_blank(),
+                   panel.grid.minor = element_blank(),
+                   panel.background = element_blank())
+
+pca$Group = paste(pca$Disease,"|", pca$Cohort,sep = "")
+Fig1a.taxa.pca
+
+Fig1a.taxa.pc1.density <-
+  ggplot(pca) +
+  geom_density(aes(x=PC1, group=Group, fill=Disease, linetype=Cohort),
+               color="black", alpha=0.6, position = 'identity') +
+  scale_fill_manual(values=c("#f0999f","#46bbc0")) +
+  theme_bw() +
+  scale_linetype_manual(values = c("solid","dashed"))+
+  labs(fill="")
+Fig1a.taxa.pc1.density
+
+Fig1a.taxa.pc2.density <-
+  ggplot(pca) +
+  geom_density(aes(x=PC2, group=Group, fill=Disease, linetype=Cohort),
+               color="black", alpha=0.6, position = 'identity') +
+  scale_fill_manual(values=c("#f0999f","#46bbc0")) +
+  theme_bw() +
+  scale_linetype_manual(values = c("solid","dashed"))+
+  labs(fill="") + 
+  coord_flip()
+Fig1a.taxa.pc2.density
+
+# Figure 1a. function #######
+
+pca <- dat.funct
+Fig1a.function.pca <- ggplot(pca,aes(PC1,PC2))+
+  geom_point(size=2, aes(col=Disease,shape=Cohort))+
+  scale_color_manual(values=c("#f0999f","#46bbc0"))+
+  scale_shape_manual(values=c(16,15)) +
+  theme_bw()+theme(axis.line = element_line(colour = "black"),
+                   panel.grid.major = element_blank(),
+                   panel.grid.minor = element_blank(),
+                   panel.background = element_blank())
+
+pca$Group = paste(pca$Disease,"|", pca$Cohort,sep = "")
+Fig1a.function.pca
+
+Fig1a.function.pc1.density <-
+  ggplot(pca) +
+  geom_density(aes(x=PC1, group=Group, fill=Disease, linetype=Cohort),
+               color="black", alpha=0.6, position = 'identity') +
+  scale_fill_manual(values=c("#f0999f","#46bbc0")) +
+  theme_bw() +
+  scale_linetype_manual(values = c("solid","dashed"))+
+  labs(fill="")
+Fig1a.function.pc1.density
+
+Fig1a.function.pc2.density <-
+  ggplot(pca) +
+  geom_density(aes(x=PC2, group=Group, fill=Disease, linetype=Cohort),
+               color="black", alpha=0.6, position = 'identity') +
+  scale_fill_manual(values=c("#f0999f","#46bbc0")) +
+  theme_bw() +
+  scale_linetype_manual(values = c("solid","dashed"))+
+  labs(fill="") + 
+  coord_flip()
+Fig1a.function.pc2.density
+
+
+
+# Figure 1b. --------------------------------------------
+rm(list = ls())
+library(reshape2)
+dat <- read_excel("Fig 1 Source Data.xlsx", sheet ="Fig 1b species abund")
+data2<-melt(dat,id.vals=c("NAME","Disease")) 
+species=factor(data2$variable,
+               levels=c("Moraxella_catarrhalis","Pseudomonas_aeruginosa","Haemophilus_parahaemolyticus","Stenotrophomonas_maltophilia","Streptococcus_intermedius","Acinetobacter_johnsonii","Neisseria_subflava","Prevotella_melaninogenica","Prevotella_intermedia","Haemophilus_parainfluenzae","Mogibacterium_diversum","Fusobacterium_pseudoperio.","Fusobacterium_nucleatum","Neisseria_flavescens","Porphyromonas_gingivalis","Veillonella_parvula","Lactobacillus_oris","Prevotella_scopos","Neisseria_meningitidis","Campylobacter_concisus","Prevotella_sp_oral_taxon_299","Neisseria_elongata","Filifactor_alocis","Prevotella_denticola","Parvimonas_micra","Treponema_sp_OMZ_838","Tannerella_sp_oral_taxon_286","Prevotella_fusca","Treponema_denticola","Tannerella_forsythia","Capnocytophaga_gingivalis"))
+Fig1b <- ggplot(data2,aes(x=species,y=data2$value),colour=factor(data2$Disease))+
+  geom_boxplot(aes(fill=data2$Disease),outlier.colour=NULL,outlier.shape=21,outlier.size=2)+
+  ylim(0,0.5)+
+  scale_fill_manual(values=c("#f0999f","#46bbc0"))+
+  xlab("") + ylab("Normalized relative abundance") +
+  theme_bw()+theme(axis.line = element_line(colour = "black"),
+                   panel.grid.major = element_blank(),
+                   panel.grid.minor = element_blank(),
+                   #  panel.border = element_blank(),
+                   panel.background = element_blank(),
+                   axis.text.x=element_text(angle=90, hjust=1, vjust=0.3, color="black",size=11),
+                   axis.text.y=element_text(color="black",size=11),
+                   axis.title.x=element_text(),
+                   axis.title.y=element_text())
+
+Fig1b