geom_point(aes(x=YFPmeans,y=ratios), size=2.5)+
geom_smooth(data=plotdf,aes(x=CFPmeans, y=ratios), method = "lm",size=0.4, se = FALSE)+
ggtitle("CFP as a proxy for copy number") +
theme_bw()+
theme(panel.grid.minor = element_blank(),panel.grid.major=element_blank(),text=element_text(size=20))+
geom_errorbarh(aes(x=CFPmeans,y=ratios,xmin=CFPmeans-CFPsds,xmax=CFPmeans+CFPsds),size=0.5,width=0.5)+
geom_errorbar(aes(x=CFPmeans,y=ratios,ymin=ratios-ratiosds,ymax=ratios+ratiosds),size=0.5,width=0.5)+
labs(x="CFP fluorescence [a.u.]",y="relative copy number (from qPCR)")
#YFP
ggplot(data=plotdf)+
geom_point(aes(x=YFPmeans,y=ratios), size=2.5)+
geom_smooth(data=plotdf,aes(x=YFPmeans, y=ratios), method = "lm",size=0.4, se = FALSE)+
ggtitle("CFP as a proxy for copy number") +
theme_bw()+
theme(panel.grid.minor = element_blank(),panel.grid.major=element_blank(),text=element_text(size=20))+
geom_errorbarh(aes(x=CFPmeans,y=ratios,xmin=CFPmeans-CFPsds,xmax=CFPmeans+CFPsds),size=0.5,width=0.5)+
geom_errorbar(aes(x=CFPmeans,y=ratios,ymin=ratios-ratiosds,ymax=ratios+ratiosds),size=0.5,width=0.5)+
labs(x="CFP fluorescence [a.u.]",y="relative copy number (from qPCR)")
#YFP
ggplot(data=plotdf)+
geom_point(aes(x=YFPmeans,y=ratios), size=2.5)+
geom_smooth(data=plotdf,aes(x=YFPmeans, y=ratios), method = "lm",size=0.4, se = FALSE)+
ggtitle("CFP as a proxy for copy number") +
theme_bw()+
theme(panel.grid.minor = element_blank(),panel.grid.major=element_blank(),text=element_text(size=20))+
geom_errorbarh(aes(x=YFPmeans,y=ratios,xmin=YFPmeans-YFPsds,xmax=YFPmeans+YFPsds),size=0.5,width=0.5)+
geom_errorbar(aes(x=YFPmeans,y=ratios,ymin=ratios-ratiosds,ymax=ratios+ratiosds),size=0.5,width=0.5)+
labs(x="CFP fluorescence [a.u.]",y="relative copy number (from qPCR)")
#YFP
ggplot(data=plotdf)+
geom_point(aes(x=YFPmeans,y=ratios), size=2.5)+
geom_smooth(data=plotdf,aes(x=YFPmeans, y=ratios), method = "lm",size=0.4, se = FALSE)+
ggtitle("CFP as a proxy for copy number") +
theme_bw()+
theme(panel.grid.minor = element_blank(),panel.grid.major=element_blank(),text=element_text(size=20))+
geom_errorbarh(aes(x=YFPmeans,y=ratios,xmin=YFPmeans-YFPsds,xmax=YFPmeans+YFPsds),size=0.5,width=0.5)+
geom_errorbar(aes(x=YFPmeans,y=ratios,ymin=ratios-ratiosds,ymax=ratios+ratiosds),size=0.5,width=0.5)+
labs(x="YFP fluorescence [a.u.]",y="relative copy number (from qPCR)")
plotdf
#CFP (switch axes to above plot)
ggplot(data=plotdf)+
geom_point(aes(x=ratios,y=CFPmeans), size=2.5)+
geom_smooth(data=plotdf,aes(x=ratios, y=CFPmeans), method = "lm",size=0.4, se = FALSE)+
ggtitle("CFP as a proxy for copy number") +
theme_bw()+
theme(panel.grid.minor = element_blank(),panel.grid.major=element_blank(),text=element_text(size=20))+
geom_errorbarh(aes(x=ratios,y=CFPmeans,xmin=ratios-ratiosds,xmax=ratios+ratiosds),size=0.5,width=0.5)+
geom_errorbar(aes(x=ratios,y=CFPmeans,ymin=CFPmeans-CFPsds,ymax=CFPmeans+CFPsds),size=0.5,width=0.5)+
labs(x="CFP fluorescence [a.u.]",y="relative copy number (from qPCR)")
#CFP (switch axes to above plot)
ggplot(data=plotdf)+
geom_point(aes(x=ratios,y=CFPmeans), size=2.5)+
geom_smooth(data=plotdf,aes(x=ratios, y=CFPmeans), method = "lm",size=0.4, se = FALSE)+
ggtitle("CFP as a proxy for copy number") +
theme_bw()+
theme(panel.grid.minor = element_blank(),panel.grid.major=element_blank(),text=element_text(size=20))+
geom_errorbarh(aes(x=ratios,y=CFPmeans,xmin=ratios-ratiosds,xmax=ratios+ratiosds),size=0.5,width=0.5)+
geom_errorbar(aes(x=ratios,y=CFPmeans,ymin=CFPmeans-CFPsds,ymax=CFPmeans+CFPsds),size=0.5,width=0.5)+
labs(x="relative copy number (from qPCR)",y="CFP fluorescence [a.u.]")
#CFP (switch axes to above plot)
ggplot(data=plotdf)+
geom_point(aes(x=ratios,y=CFPmeans), size=2.5)+
geom_smooth(data=plotdf,aes(x=ratios, y=CFPmeans), method = "lm",size=1, se = FALSE)+
ggtitle("CFP as a proxy for copy number") +
theme_bw()+
theme(panel.grid.minor = element_blank(),panel.grid.major=element_blank(),text=element_text(size=20))+
geom_errorbarh(aes(x=ratios,y=CFPmeans,xmin=ratios-ratiosds,xmax=ratios+ratiosds),size=0.5,width=0.5)+
geom_errorbar(aes(x=ratios,y=CFPmeans,ymin=CFPmeans-CFPsds,ymax=CFPmeans+CFPsds),size=0.5,width=0.5)+
labs(x="relative copy number (from qPCR)",y="CFP fluorescence [a.u.]")
#CFP (switch axes to above plot)
ggplot(data=plotdf)+
geom_point(aes(x=ratios,y=CFPmeans), size=2.5)+
geom_smooth(data=plotdf,aes(x=ratios, y=CFPmeans), method = "lm",size=1, se = FALSE,color="orange")+
ggtitle("CFP as a proxy for copy number") +
theme_bw()+
theme(panel.grid.minor = element_blank(),panel.grid.major=element_blank(),text=element_text(size=20))+
geom_errorbarh(aes(x=ratios,y=CFPmeans,xmin=ratios-ratiosds,xmax=ratios+ratiosds),size=0.5,width=0.5)+
geom_errorbar(aes(x=ratios,y=CFPmeans,ymin=CFPmeans-CFPsds,ymax=CFPmeans+CFPsds),size=0.5,width=0.5)+
labs(x="relative copy number (from qPCR)",y="CFP fluorescence [a.u.]")
#CFP (switch axes to above plot)
ggplot(data=plotdf)+
geom_point(aes(x=ratios,y=CFPmeans), size=2.5)+
geom_smooth(data=plotdf,aes(x=ratios, y=CFPmeans), method = "lm",size=1, se = FALSE,color="blue")+
ggtitle("CFP as a proxy for copy number") +
theme_bw()+
theme(panel.grid.minor = element_blank(),panel.grid.major=element_blank(),text=element_text(size=20))+
geom_errorbarh(aes(x=ratios,y=CFPmeans,xmin=ratios-ratiosds,xmax=ratios+ratiosds),size=0.5,width=0.5)+
geom_errorbar(aes(x=ratios,y=CFPmeans,ymin=CFPmeans-CFPsds,ymax=CFPmeans+CFPsds),size=0.5,width=0.5)+
labs(x="relative copy number (from qPCR)",y="CFP fluorescence [a.u.]")
#YFP
ggplot(data=plotdf)+
geom_point(aes(x=YFPmeans,y=ratios), size=2.5)+
geom_smooth(data=plotdf,aes(x=YFPmeans, y=ratios), method = "lm",size=1, se = FALSE,color="orange")+
ggtitle("CFP as a proxy for copy number") +
theme_bw()+
theme(panel.grid.minor = element_blank(),panel.grid.major=element_blank(),text=element_text(size=20))+
geom_errorbarh(aes(x=YFPmeans,y=ratios,xmin=YFPmeans-YFPsds,xmax=YFPmeans+YFPsds),size=0.5,width=0.5)+
geom_errorbar(aes(x=YFPmeans,y=ratios,ymin=ratios-ratiosds,ymax=ratios+ratiosds),size=0.5,width=0.5)+
labs(x="YFP fluorescence [a.u.]",y="relative copy number (from qPCR)")
ratios_all
ratiosds
plotdf=data.frame(ratios,CFPmeans,ratiosds,CFPsds,YFPmeans,YFPsds)
plotdf
plotdf=data.frame(samplelist,ratios,CFPmeans,ratiosds,CFPsds,YFPmeans,YFPsds)
plotdf
#CFP (switch axes to above plot)
ggplot(data=subset(plotdf,samplelist!="9"))+
geom_point(aes(x=ratios,y=CFPmeans), size=2.5)+
geom_smooth(data=plotdf,aes(x=ratios, y=CFPmeans), method = "lm",size=1, se = FALSE,color="blue")+
ggtitle("CFP as a proxy for copy number") +
theme_bw()+
theme(panel.grid.minor = element_blank(),panel.grid.major=element_blank(),text=element_text(size=20))+
geom_errorbarh(aes(x=ratios,y=CFPmeans,xmin=ratios-ratiosds,xmax=ratios+ratiosds),size=0.5,width=0.5)+
geom_errorbar(aes(x=ratios,y=CFPmeans,ymin=CFPmeans-CFPsds,ymax=CFPmeans+CFPsds),size=0.5,width=0.5)+
labs(x="relative copy number (from qPCR)",y="CFP fluorescence [a.u.]")
#YFP
ggplot(data=subset(plotdf,sampleslist!="7"))+  #exclude promoter mut.from stats, plot individually
geom_point(aes(x=YFPmeans,y=ratios), size=2.5)+
geom_smooth(data=plotdf,aes(x=YFPmeans, y=ratios), method = "lm",size=1, se = FALSE,color="orange")+
ggtitle("CFP as a proxy for copy number") +
theme_bw()+
theme(panel.grid.minor = element_blank(),panel.grid.major=element_blank(),text=element_text(size=20))+
geom_errorbarh(aes(x=YFPmeans,y=ratios,xmin=YFPmeans-YFPsds,xmax=YFPmeans+YFPsds),size=0.5,width=0.5)+
geom_errorbar(aes(x=YFPmeans,y=ratios,ymin=ratios-ratiosds,ymax=ratios+ratiosds),size=0.5,width=0.5)+
labs(x="YFP fluorescence [a.u.]",y="relative copy number (from qPCR)")
#YFP
ggplot(data=subset(plotdf,samplelist!="7"))+  #exclude promoter mut.from stats, plot individually
geom_point(aes(x=YFPmeans,y=ratios), size=2.5)+
geom_smooth(data=plotdf,aes(x=YFPmeans, y=ratios), method = "lm",size=1, se = FALSE,color="orange")+
ggtitle("CFP as a proxy for copy number") +
theme_bw()+
theme(panel.grid.minor = element_blank(),panel.grid.major=element_blank(),text=element_text(size=20))+
geom_errorbarh(aes(x=YFPmeans,y=ratios,xmin=YFPmeans-YFPsds,xmax=YFPmeans+YFPsds),size=0.5,width=0.5)+
geom_errorbar(aes(x=YFPmeans,y=ratios,ymin=ratios-ratiosds,ymax=ratios+ratiosds),size=0.5,width=0.5)+
labs(x="YFP fluorescence [a.u.]",y="relative copy number (from qPCR)")
#YFP
ggplot(data=subset(plotdf,samplelist!="7"))+  #exclude promoter mut.from stats, plot individually
geom_point(aes(x=YFPmeans,y=ratios), size=2.5)+
geom_smooth(data=subset(plotdf,samplelist!="7"),aes(x=YFPmeans, y=ratios), method = "lm",size=1, se = FALSE,color="orange")+
ggtitle("CFP as a proxy for copy number") +
theme_bw()+
theme(panel.grid.minor = element_blank(),panel.grid.major=element_blank(),text=element_text(size=20))+
geom_errorbarh(aes(x=YFPmeans,y=ratios,xmin=YFPmeans-YFPsds,xmax=YFPmeans+YFPsds),size=0.5,width=0.5)+
geom_errorbar(aes(x=YFPmeans,y=ratios,ymin=ratios-ratiosds,ymax=ratios+ratiosds),size=0.5,width=0.5)+
labs(x="YFP fluorescence [a.u.]",y="relative copy number (from qPCR)")
#YFP
ggplot(data=subset(plotdf))+  #exclude promoter mut.from stats, plot individually
geom_point(aes(x=YFPmeans,y=ratios), size=2.5)+
geom_smooth(data=subset(plotdf,samplelist!="7"),aes(x=YFPmeans, y=ratios), method = "lm",size=1, se = FALSE,color="orange")+
ggtitle("CFP as a proxy for copy number") +
theme_bw()+
theme(panel.grid.minor = element_blank(),panel.grid.major=element_blank(),text=element_text(size=20))+
geom_errorbarh(aes(x=YFPmeans,y=ratios,xmin=YFPmeans-YFPsds,xmax=YFPmeans+YFPsds),size=0.5,width=0.5)+
geom_errorbar(aes(x=YFPmeans,y=ratios,ymin=ratios-ratiosds,ymax=ratios+ratiosds),size=0.5,width=0.5)+
labs(x="YFP fluorescence [a.u.]",y="relative copy number (from qPCR)")
#YFP
ggplot(data=subset(plotdf))+
geom_point(aes(x=YFPmeans,y=ratios), size=2.5)+
geom_point(data=subset(plotdf,samplelist=="7"),aes(x=YFPmeans,y=ratios), size=2.5,color="promoter mutant")+
#exclude promoter mut.from stats, plot individually
geom_smooth(data=subset(plotdf,samplelist!="7"),aes(x=YFPmeans, y=ratios), method = "lm",size=1, se = FALSE,color="orange")+
ggtitle("CFP as a proxy for copy number") +
theme_bw()+
theme(panel.grid.minor = element_blank(),panel.grid.major=element_blank(),text=element_text(size=20))+
geom_errorbarh(aes(x=YFPmeans,y=ratios,xmin=YFPmeans-YFPsds,xmax=YFPmeans+YFPsds),size=0.5,width=0.5)+
geom_errorbar(aes(x=YFPmeans,y=ratios,ymin=ratios-ratiosds,ymax=ratios+ratiosds),size=0.5,width=0.5)+
labs(x="YFP fluorescence [a.u.]",y="relative copy number (from qPCR)")
#YFP
ggplot(data=subset(plotdf))+
geom_point(aes(x=YFPmeans,y=ratios), size=2.5)+
geom_point(data=subset(plotdf,samplelist=="7"),aes(x=YFPmeans,y=ratios), size=2.5,color="green")+
#exclude promoter mut.from stats, plot individually
geom_smooth(data=subset(plotdf,samplelist!="7"),aes(x=YFPmeans, y=ratios), method = "lm",size=1, se = FALSE,color="orange")+
ggtitle("CFP as a proxy for copy number") +
theme_bw()+
theme(panel.grid.minor = element_blank(),panel.grid.major=element_blank(),text=element_text(size=20))+
geom_errorbarh(aes(x=YFPmeans,y=ratios,xmin=YFPmeans-YFPsds,xmax=YFPmeans+YFPsds),size=0.5,width=0.5)+
geom_errorbar(aes(x=YFPmeans,y=ratios,ymin=ratios-ratiosds,ymax=ratios+ratiosds),size=0.5,width=0.5)+
labs(x="YFP fluorescence [a.u.]",y="relative copy number (from qPCR)")
#CFP (switch axes to above plot)
ggplot(data=plotdf)+
geom_point(aes(x=ratios,y=CFPmeans), size=2.5)+
geom_smooth(data=plotdf,aes(x=ratios, y=CFPmeans), method = "lm",size=1, se = FALSE,color="blue")+
ggtitle("CFP as a proxy for copy number") +
theme_bw()+
theme(panel.grid.minor = element_blank(),panel.grid.major=element_blank(),text=element_text(size=20))+
geom_errorbarh(aes(x=ratios,y=CFPmeans,xmin=ratios-ratiosds,xmax=ratios+ratiosds),size=0.5,width=0.5)+
geom_errorbar(aes(x=ratios,y=CFPmeans,ymin=CFPmeans-CFPsds,ymax=CFPmeans+CFPsds),size=0.5,width=0.5)+
labs(x="relative copy number (from qPCR)",y="CFP fluorescence [a.u.]")
#YFP
#YFP (switch axes to above plot)
ggplot(data=plotdf)+
geom_point(aes(x=ratios,y=YFPmeans), size=2.5)+
geom_point(data=subset(plotdf,samplelist=="7"),aes(x=ratios,y=YFPmeans), size=2.5,color="green")+
#exclude promoter mut.from stats, plot individually
geom_smooth(data=subset(plotdf,samplelist!="7"),aes(x=ratios, y=YFPmeans), method = "lm",size=1, se = FALSE,color="blue")+
ggtitle("YFP as a proxy for copy number") +
theme_bw()+
theme(panel.grid.minor = element_blank(),panel.grid.major=element_blank(),text=element_text(size=20))+
geom_errorbarh(aes(x=ratios,y=YFPmeans,xmin=ratios-ratiosds,xmax=ratios+ratiosds),size=0.5,width=0.5)+
geom_errorbar(aes(x=ratios,y=YFPmeans,ymin=YFPmeans-YFPsds,ymax=YFPmeans+YFPsds),size=0.5,width=0.5)+
labs(x="relative copy number (from qPCR)",y="YFP fluorescence [a.u.]")
#YFP
#YFP (switch axes to above plot)
ggplot(data=plotdf)+
geom_point(aes(x=ratios,y=YFPmeans), size=2.5)+
geom_point(data=subset(plotdf,samplelist=="7"),aes(x=ratios,y=YFPmeans), size=2.5,color="green")+
#exclude promoter mut.from stats, plot individually
geom_smooth(data=subset(plotdf,samplelist!="7"),aes(x=ratios, y=YFPmeans), method = "lm",size=1, se = FALSE,color="orange")+
ggtitle("YFP as a proxy for copy number") +
theme_bw()+
theme(panel.grid.minor = element_blank(),panel.grid.major=element_blank(),text=element_text(size=20))+
geom_errorbarh(aes(x=ratios,y=YFPmeans,xmin=ratios-ratiosds,xmax=ratios+ratiosds),size=0.5,width=0.5)+
geom_errorbar(aes(x=ratios,y=YFPmeans,ymin=YFPmeans-YFPsds,ymax=YFPmeans+YFPsds),size=0.5,width=0.5)+
labs(x="relative copy number (from qPCR)",y="YFP fluorescence [a.u.]")
#YFP and CFP
ggplot(data=plotdf)+
geom_point(aes(x=CFPmeans,y=YFPmeans), size=2.5)+
geom_point(data=subset(plotdf,samplelist=="7"),aes(x=CFPmeans,y=YFPmeans), size=2.5,color="green")+
#exclude promoter mut.from stats, plot individually
geom_smooth(data=subset(plotdf,samplelist!="7"),aes(x=CFPmeans, y=YFPmeans), method = "lm",size=1, se = FALSE,color="orange")+
ggtitle("YFP as a proxy for copy number") +
theme_bw()+
theme(panel.grid.minor = element_blank(),panel.grid.major=element_blank(),text=element_text(size=20))+
geom_errorbarh(aes(x=CFPmeans,y=YFPmeans,xmin=CFPmeans-CFPsds,xmax=CFPmeans+CFPsds),size=0.5,width=0.5)+
geom_errorbar(aes(x=ratios,y=YFPmeans,ymin=YFPmeans-YFPsds,ymax=YFPmeans+YFPsds),size=0.5,width=0.5)+
labs(x="relative copy number (from qPCR)",y="YFP fluorescence [a.u.]")
#YFP and CFP
ggplot(data=plotdf)+
geom_point(aes(x=CFPmeans,y=YFPmeans), size=2.5)+
geom_point(data=subset(plotdf,samplelist=="7"),aes(x=CFPmeans,y=YFPmeans), size=2.5,color="green")+
#exclude promoter mut.from stats, plot individually
geom_smooth(data=subset(plotdf,samplelist!="7"),aes(x=CFPmeans, y=YFPmeans), method = "lm",size=1, se = FALSE,color="green")+
ggtitle("YFP as a proxy for copy number") +
theme_bw()+
theme(panel.grid.minor = element_blank(),panel.grid.major=element_blank(),text=element_text(size=20))+
geom_errorbarh(aes(x=CFPmeans,y=YFPmeans,xmin=CFPmeans-CFPsds,xmax=CFPmeans+CFPsds),size=0.5,width=0.5)+
geom_errorbar(aes(x=YFPmeans,y=YFPmeans,ymin=YFPmeans-YFPsds,ymax=YFPmeans+YFPsds),size=0.5,width=0.5)+
labs(x="relative copy number (from qPCR)",y="YFP fluorescence [a.u.]")
#YFP and CFP
ggplot(data=plotdf)+
geom_point(aes(x=CFPmeans,y=YFPmeans), size=2.5)+
geom_point(data=subset(plotdf,samplelist=="7"),aes(x=CFPmeans,y=YFPmeans), size=2.5,color="green")+
#exclude promoter mut.from stats, plot individually
geom_smooth(data=subset(plotdf,samplelist!="7"),aes(x=CFPmeans, y=YFPmeans), method = "lm",size=1, se = FALSE,color="green")+
ggtitle("YFP as a proxy for copy number") +
theme_bw()+
theme(panel.grid.minor = element_blank(),panel.grid.major=element_blank(),text=element_text(size=20))+
geom_errorbarh(aes(x=CFPmeans,y=YFPmeans,xmin=CFPmeans-CFPsds,xmax=CFPmeans+CFPsds),size=0.5,width=0.5)+
geom_errorbar(aes(x=CFPmeans,y=YFPmeans,ymin=YFPmeans-YFPsds,ymax=YFPmeans+YFPsds),size=0.5,width=0.5)+
labs(x="relative copy number (from qPCR)",y="YFP fluorescence [a.u.]")
#YFP and CFP
ggplot(data=plotdf)+
geom_point(aes(x=CFPmeans,y=YFPmeans), size=2.5)+
geom_point(data=subset(plotdf,samplelist=="7"),aes(x=CFPmeans,y=YFPmeans), size=2.5,color="green")+
#exclude promoter mut.from stats, plot individually
geom_smooth(data=subset(plotdf,samplelist!="7"),aes(x=CFPmeans, y=YFPmeans), method = "lm",size=1, se = FALSE,color="green")+
ggtitle("YFP as a proxy for copy number") +
theme_bw()+
theme(panel.grid.minor = element_blank(),panel.grid.major=element_blank(),text=element_text(size=20))+
geom_errorbarh(aes(x=CFPmeans,y=YFPmeans,xmin=CFPmeans-CFPsds,xmax=CFPmeans+CFPsds),size=0.5,width=0.5)+
geom_errorbar(aes(x=CFPmeans,y=YFPmeans,ymin=YFPmeans-YFPsds,ymax=YFPmeans+YFPsds),size=0.5,width=0.5)+
labs(x="CFP fluorescence [a.u.]",y="YFP fluorescence [a.u.]")
#YFP and CFP
ggplot(data=plotdf)+
geom_point(aes(x=CFPmeans,y=YFPmeans), size=2.5)+
geom_point(data=subset(plotdf,samplelist=="7"),aes(x=CFPmeans,y=YFPmeans), size=2.5,color="green")+
#exclude promoter mut.from stats, plot individually
geom_smooth(data=subset(plotdf,samplelist!="7"),aes(x=CFPmeans, y=YFPmeans), method = "lm",size=1, se = FALSE,color="dark green")+
ggtitle("YFP as a proxy for copy number") +
theme_bw()+
theme(panel.grid.minor = element_blank(),panel.grid.major=element_blank(),text=element_text(size=20))+
geom_errorbarh(aes(x=CFPmeans,y=YFPmeans,xmin=CFPmeans-CFPsds,xmax=CFPmeans+CFPsds),size=0.5,width=0.5)+
geom_errorbar(aes(x=CFPmeans,y=YFPmeans,ymin=YFPmeans-YFPsds,ymax=YFPmeans+YFPsds),size=0.5,width=0.5)+
labs(x="CFP fluorescence [a.u.]",y="YFP fluorescence [a.u.]")
#YFP and CFP
ggplot(data=plotdf)+
geom_point(aes(x=CFPmeans,y=YFPmeans), size=2.5)+
geom_point(data=subset(plotdf,samplelist=="7"),aes(x=CFPmeans,y=YFPmeans), size=2.5,color="green")+
#exclude promoter mut.from stats, plot individually
geom_smooth(data=subset(plotdf,samplelist!="7"),aes(x=CFPmeans, y=YFPmeans), method = "lm",size=1, se = FALSE,color="dark green")+
ggtitle("colony phenotype") +
theme_bw()+
theme(panel.grid.minor = element_blank(),panel.grid.major=element_blank(),text=element_text(size=20))+
geom_errorbarh(aes(x=CFPmeans,y=YFPmeans,xmin=CFPmeans-CFPsds,xmax=CFPmeans+CFPsds),size=0.5,width=0.5)+
geom_errorbar(aes(x=CFPmeans,y=YFPmeans,ymin=YFPmeans-YFPsds,ymax=YFPmeans+YFPsds),size=0.5,width=0.5)+
labs(x="CFP fluorescence [a.u.]",y="YFP fluorescence [a.u.]")
#hindrance paper
#CFP (switch axes to above plot)
a=ggplot(data=plotdf)+
geom_point(aes(x=ratios,y=CFPmeans), size=2.5)+
geom_smooth(data=plotdf,aes(x=ratios, y=CFPmeans), method = "lm",size=1, se = FALSE,color="blue")+
ggtitle("CFP as a proxy for copy number") +
theme_bw()+
theme(panel.grid.minor = element_blank(),panel.grid.major=element_blank(),text=element_text(size=20))+
geom_errorbarh(aes(x=ratios,y=CFPmeans,xmin=ratios-ratiosds,xmax=ratios+ratiosds),size=0.5,width=0.5)+
geom_errorbar(aes(x=ratios,y=CFPmeans,ymin=CFPmeans-CFPsds,ymax=CFPmeans+CFPsds),size=0.5,width=0.5)+
labs(x="relative copy number (from qPCR)",y="CFP fluorescence [a.u.]")
#YFP
#YFP (switch axes to above plot)
b=ggplot(data=plotdf)+
geom_point(aes(x=ratios,y=YFPmeans), size=2.5)+
geom_point(data=subset(plotdf,samplelist=="7"),aes(x=ratios,y=YFPmeans), size=2.5,color="green")+
#exclude promoter mut.from stats, plot individually
geom_smooth(data=subset(plotdf,samplelist!="7"),aes(x=ratios, y=YFPmeans), method = "lm",size=1, se = FALSE,color="orange")+
ggtitle("YFP as a proxy for copy number") +
theme_bw()+
theme(panel.grid.minor = element_blank(),panel.grid.major=element_blank(),text=element_text(size=20))+
geom_errorbarh(aes(x=ratios,y=YFPmeans,xmin=ratios-ratiosds,xmax=ratios+ratiosds),size=0.5,width=0.5)+
geom_errorbar(aes(x=ratios,y=YFPmeans,ymin=YFPmeans-YFPsds,ymax=YFPmeans+YFPsds),size=0.5,width=0.5)+
labs(x="relative copy number (from qPCR)",y="YFP fluorescence [a.u.]")
#YFP and CFP
c=ggplot(data=plotdf)+
geom_point(aes(x=CFPmeans,y=YFPmeans), size=2.5)+
geom_point(data=subset(plotdf,samplelist=="7"),aes(x=CFPmeans,y=YFPmeans), size=2.5,color="green")+
#exclude promoter mut.from stats, plot individually
geom_smooth(data=subset(plotdf,samplelist!="7"),aes(x=CFPmeans, y=YFPmeans), method = "lm",size=1, se = FALSE,color="dark green")+
ggtitle("colony phenotype") +
theme_bw()+
theme(panel.grid.minor = element_blank(),panel.grid.major=element_blank(),text=element_text(size=20))+
geom_errorbarh(aes(x=CFPmeans,y=YFPmeans,xmin=CFPmeans-CFPsds,xmax=CFPmeans+CFPsds),size=0.5,width=0.5)+
geom_errorbar(aes(x=CFPmeans,y=YFPmeans,ymin=YFPmeans-YFPsds,ymax=YFPmeans+YFPsds),size=0.5,width=0.5)+
labs(x="CFP fluorescence [a.u.]",y="YFP fluorescence [a.u.]")
multiplot(a,b,c,cols=1)
library("Rmisc")
multiplot(a,b,c,cols=1)
library("Rmisc")
a
b
c
#hindrance paper
#CFP (switch axes to above plot)
a=ggplot(data=plotdf)+
geom_point(data=subset(plotdf,samplelist=="7"),aes(x=CFPmeans,y=YFPmeans), size=2.5,color="green")+
geom_point(aes(x=ratios,y=CFPmeans), size=2.5)+
geom_smooth(data=plotdf,aes(x=ratios, y=CFPmeans), method = "lm",size=1, se = FALSE,color="blue")+
ggtitle("CFP as a proxy for copy number") +
theme_bw()+
theme(panel.grid.minor = element_blank(),panel.grid.major=element_blank(),text=element_text(size=20))+
geom_errorbarh(aes(x=ratios,y=CFPmeans,xmin=ratios-ratiosds,xmax=ratios+ratiosds),size=0.5,width=0.5)+
geom_errorbar(aes(x=ratios,y=CFPmeans,ymin=CFPmeans-CFPsds,ymax=CFPmeans+CFPsds),size=0.5,width=0.5)+
labs(x="relative copy number (from qPCR)",y="CFP fluorescence [a.u.]")
#hindrance paper
#CFP (switch axes to above plot)
a=ggplot(data=plotdf)+
geom_point(data=subset(plotdf,samplelist=="7"),aes(x=CFPmeans,y=YFPmeans), size=2.5,color="green")+
geom_point(aes(x=ratios,y=CFPmeans), size=2.5)+
geom_smooth(data=plotdf,aes(x=ratios, y=CFPmeans), method = "lm",size=1, se = FALSE,color="blue")+
ggtitle("CFP as a proxy for copy number") +
theme_bw()+
theme(panel.grid.minor = element_blank(),panel.grid.major=element_blank(),text=element_text(size=20))+
geom_errorbarh(aes(x=ratios,y=CFPmeans,xmin=ratios-ratiosds,xmax=ratios+ratiosds),size=0.5,width=0.5)+
geom_errorbar(aes(x=ratios,y=CFPmeans,ymin=CFPmeans-CFPsds,ymax=CFPmeans+CFPsds),size=0.5,width=0.5)+
labs(x="relative copy number (from qPCR)",y="CFP fluorescence [a.u.]")
#hindrance paper
#CFP (switch axes to above plot)
a=ggplot(data=plotdf)+
geom_point(data=subset(plotdf,samplelist=="7"),aes(x=CFPmeans,y=YFPmeans), size=2.5,color="green")+
geom_point(aes(x=ratios,y=CFPmeans), size=2.5)+
geom_smooth(data=plotdf,aes(x=ratios, y=CFPmeans), method = "lm",size=1, se = FALSE,color="blue")+
ggtitle("CFP as a proxy for copy number") +
theme_bw()+
theme(panel.grid.minor = element_blank(),panel.grid.major=element_blank(),text=element_text(size=20))+
geom_errorbarh(aes(x=ratios,y=CFPmeans,xmin=ratios-ratiosds,xmax=ratios+ratiosds),size=0.5,width=0.5)+
geom_errorbar(aes(x=ratios,y=CFPmeans,ymin=CFPmeans-CFPsds,ymax=CFPmeans+CFPsds),size=0.5,width=0.5)+
labs(x="relative copy number (from qPCR)",y="CFP fluorescence [a.u.]")
a
#hindrance paper
#CFP (switch axes to above plot)
a=ggplot(data=plotdf)+
geom_point(data=subset(plotdf,samplelist=="7"),aes(x=CFPmeans,y=ratios), size=2.5,color="green")+
geom_point(aes(x=ratios,y=CFPmeans), size=2.5)+
geom_smooth(data=plotdf,aes(x=ratios, y=CFPmeans), method = "lm",size=1, se = FALSE,color="blue")+
ggtitle("CFP as a proxy for copy number") +
theme_bw()+
theme(panel.grid.minor = element_blank(),panel.grid.major=element_blank(),text=element_text(size=20))+
geom_errorbarh(aes(x=ratios,y=CFPmeans,xmin=ratios-ratiosds,xmax=ratios+ratiosds),size=0.5,width=0.5)+
geom_errorbar(aes(x=ratios,y=CFPmeans,ymin=CFPmeans-CFPsds,ymax=CFPmeans+CFPsds),size=0.5,width=0.5)+
labs(x="relative copy number (from qPCR)",y="CFP fluorescence [a.u.]")
#hindrance paper
#CFP (switch axes to above plot)
a=ggplot(data=plotdf)+
geom_point(data=subset(plotdf,samplelist=="7"),aes(x=ratios,y=CFPmeans), size=2.5,color="green")+
geom_point(aes(x=ratios,y=CFPmeans), size=2.5)+
geom_smooth(data=plotdf,aes(x=ratios, y=CFPmeans), method = "lm",size=1, se = FALSE,color="blue")+
ggtitle("CFP as a proxy for copy number") +
theme_bw()+
theme(panel.grid.minor = element_blank(),panel.grid.major=element_blank(),text=element_text(size=20))+
geom_errorbarh(aes(x=ratios,y=CFPmeans,xmin=ratios-ratiosds,xmax=ratios+ratiosds),size=0.5,width=0.5)+
geom_errorbar(aes(x=ratios,y=CFPmeans,ymin=CFPmeans-CFPsds,ymax=CFPmeans+CFPsds),size=0.5,width=0.5)+
labs(x="relative copy number (from qPCR)",y="CFP fluorescence [a.u.]")
a
a
#hindrance paper
#CFP (switch axes to above plot)
a=ggplot(data=plotdf)+
geom_point(aes(x=ratios,y=CFPmeans), size=2.5)+
geom_smooth(data=plotdf,aes(x=ratios, y=CFPmeans), method = "lm",size=1, se = FALSE,color="blue")+
ggtitle("CFP as a proxy for copy number") +
theme_bw()+
theme(panel.grid.minor = element_blank(),panel.grid.major=element_blank(),text=element_text(size=20))+
geom_errorbarh(aes(x=ratios,y=CFPmeans,xmin=ratios-ratiosds,xmax=ratios+ratiosds),size=0.5,width=0.5)+
geom_errorbar(aes(x=ratios,y=CFPmeans,ymin=CFPmeans-CFPsds,ymax=CFPmeans+CFPsds),size=0.5,width=0.5)+
labs(x="relative copy number (from qPCR)",y="CFP fluorescence [a.u.]")
#hindrance paper
#CFP (switch axes to above plot)
a=ggplot(data=plotdf)+
geom_point(aes(x=ratios,y=CFPmeans), size=2.5)+
geom_point(data=subset(plotdf,samplelist=="7"),aes(x=ratios,y=CFPmeans), size=2.5,color="green")+
geom_smooth(data=plotdf,aes(x=ratios, y=CFPmeans), method = "lm",size=1, se = FALSE,color="blue")+
ggtitle("CFP as a proxy for copy number") +
theme_bw()+
theme(panel.grid.minor = element_blank(),panel.grid.major=element_blank(),text=element_text(size=20))+
geom_errorbarh(aes(x=ratios,y=CFPmeans,xmin=ratios-ratiosds,xmax=ratios+ratiosds),size=0.5,width=0.5)+
geom_errorbar(aes(x=ratios,y=CFPmeans,ymin=CFPmeans-CFPsds,ymax=CFPmeans+CFPsds),size=0.5,width=0.5)+
labs(x="relative copy number (from qPCR)",y="CFP fluorescence [a.u.]")
a
#YFP
#YFP (switch axes to above plot)
b=ggplot(data=plotdf)+
geom_point(aes(x=ratios,y=YFPmeans), size=2.5)+
geom_point(data=subset(plotdf,samplelist=="7"),aes(x=ratios,y=YFPmeans), size=2.5,color="green")+
#exclude promoter mut.from stats, plot individually
geom_smooth(data=subset(plotdf,samplelist!="7"),aes(x=ratios, y=YFPmeans), method = "lm",size=1, se = FALSE,color="orange")+
ggtitle("YFP as a proxy for copy number") +
theme_bw()+
theme(panel.grid.minor = element_blank(),panel.grid.major=element_blank(),text=element_text(size=20))+
geom_errorbarh(aes(x=ratios,y=YFPmeans,xmin=ratios-ratiosds,xmax=ratios+ratiosds),size=0.5,width=0.5)+
geom_errorbar(aes(x=ratios,y=YFPmeans,ymin=YFPmeans-YFPsds,ymax=YFPmeans+YFPsds),size=0.5,width=0.5)+
labs(x="relative copy number (from qPCR)",y="YFP fluorescence [a.u.]")
b
#YFP and CFP
c=ggplot(data=plotdf)+
geom_point(aes(x=CFPmeans,y=YFPmeans), size=2.5)+
geom_point(data=subset(plotdf,samplelist=="7"),aes(x=CFPmeans,y=YFPmeans), size=2.5,color="green")+
#exclude promoter mut.from stats, plot individually
geom_smooth(data=subset(plotdf,samplelist!="7"),aes(x=CFPmeans, y=YFPmeans), method = "lm",size=1, se = FALSE,color="dark green")+
ggtitle("colony phenotype") +
theme_bw()+
theme(panel.grid.minor = element_blank(),panel.grid.major=element_blank(),text=element_text(size=20))+
geom_errorbarh(aes(x=CFPmeans,y=YFPmeans,xmin=CFPmeans-CFPsds,xmax=CFPmeans+CFPsds),size=0.5,width=0.5)+
geom_errorbar(aes(x=CFPmeans,y=YFPmeans,ymin=YFPmeans-YFPsds,ymax=YFPmeans+YFPsds),size=0.5,width=0.5)+
labs(x="CFP fluorescence [a.u.]",y="YFP fluorescence [a.u.]")
b
c
### Revision Hindrance paper, highlight sequenced day 7 populations
# YFP-CFP plot
ggplot()+
geom_point(data=subset(grouped_E), aes(x=log(CFP), y=log(YFP),   group=Well),col="grey",alpha=0.8)+
geom_point(data=subset(grouped_E,Time=="6.08"&Well=="E7"), aes(x=log(CFP), y=log(YFP),   group=Well),color="cyan")+
geom_point(data=subset(grouped_E,Time=="6.08"&Well=="D5"), aes(x=log(CFP), y=log(YFP),   group=Well),color="cyan")+
geom_point(data=subset(grouped_A), aes(x=log(CFP), y=log(YFP),   group=Well),alpha=0.8)+
geom_point(data=subset(grouped_A,Time=="6.08"&Well=="A3"), aes(x=log(CFP), y=log(YFP),   group=Well),color="cyan")+
geom_point(data=subset(grouped_A,Time=="6.08"&Well=="D5"), aes(x=log(CFP), y=log(YFP),   group=Well),color="cyan")+
geom_point(data=subset(grouped_A,Time=="6.08"&Well=="F6"), aes(x=log(CFP), y=log(YFP),   group=Well),color="cyan")+
geom_point(data=subset(grouped_B), aes(x=log(CFP), y=log(YFP),   group=Well),alpha=0.8)+
geom_point(data=subset(grouped_B,Time=="6.08"&Well=="A3"), aes(x=log(CFP), y=log(YFP),  group=Well),color=" magenta" )+
geom_point(data=subset(grouped_B,Time=="6.08"&Well=="D4"), aes(x=log(CFP), y=log(YFP),  group=Well),color="magenta" )+
geom_point(data=subset(grouped_B,Time=="6.08"&Well=="G9"), aes(x=log(CFP), y=log(YFP),  group=Well),color="cyan" )+
geom_point(data=subset(grouped_C), aes(x=log(CFP), y=log(YFP),   group=Well),alpha=0.8)+
geom_point(data=subset(grouped_C,Time=="6.08"&Well=="H1"), aes(x=log(CFP), y=log(YFP),  group=Well),color="cyan" )+
geom_point(data=subset(grouped_C,Time=="6.08"&Well=="A8"), aes(x=log(CFP), y=log(YFP),  group=Well),color="cyan" )+
geom_point(data=subset(grouped_C,Time=="6.08"&Well=="B5"), aes(x=log(CFP), y=log(YFP),  group=Well),color="magenta" )+
#geom_point(data=subset(grouped_C), aes(x=log(CFP), y=log(YFP),  color=as.factor(medium), group=Well))+
theme_bw()+  #no grey background
theme(panel.grid.minor = element_blank(),panel.grid.major=element_blank(),text=element_text(size=15)) +
facet_wrap(~ medium)
## normalize by OD! --> NO PROMOTER MUTANTS :DD (which is what the streaks looked like :)
## CFP-YFP plot (log-log to see low copy high YFP fraction)
ggplot()+
theme_bw()+  #no grey background
theme(panel.grid.minor = element_blank(),panel.grid.major=element_blank(),text=element_text(size=15)) +
geom_point(data=grouped_A, aes(x=(CFP/OD600), y=(YFP/OD600), group=Well, shape=as.factor(time),color=as.factor(medium)),alpha=0.9,size=4)+
geom_point(data=grouped_B, aes(x=(CFP/OD600), y=(YFP/OD600), group=Well, shape=as.factor(time), color=as.factor(medium)),alpha=0.9,size=4)+
geom_point(data=grouped_C, aes(x=(CFP/OD600), y=(YFP/OD600), group=Well, shape=as.factor(time),color=as.factor(medium)),alpha=0.9,size=4)+
geom_point(data=grouped_E, aes(x=(CFP/OD600), y=(YFP/OD600), group=Well,shape=as.factor(time), color=as.factor(medium)),alpha=0.9,size=4)+
scale_shape_identity()
plot(CFPmeans,YFPmeans, ylab="relative copy #  -- as determined by qPCR", xlab="CFP fluorescene of colony [RFU]", main="CFP fluorescence as proxy for copy nr.")
abline(lm(ratios~YFPmeans))  #promoter mutant H5 is an outlier (as expected)
YFPmeans
YFPmeans[c(1:6,8:9)]
#for YFP stats exclude the promoter mutant: YFPmeans[c(1:6,8:9)]
plot(CFPmeans[c(1:6,8:9)],YFPmeans[c(1:6,8:9)], ylab="relative copy #  -- as determined by qPCR", xlab="CFP fluorescene of colony [RFU]", main="CFP fluorescence as proxy for copy nr.")
abline(lm(ratios~YFPmeans))  #promoter mutant H5 is an outlier (as expected)
summary((lm(ratios~CFPmeans)))
#for YFP stats exclude the promoter mutant: YFPmeans[c(1:6,8:9)]
plot(CFPmeans[c(1:6,8:9)],YFPmeans[c(1:6,8:9)], ylab="relative copy #  -- as determined by qPCR", xlab="CFP fluorescene of colony [RFU]", main="CFP fluorescence as proxy for copy nr.")
abline(lm(ratios~YFPmeans))  #promoter mutant H5 is an outlier (as expected)
summary((lm(ratios~CFPmeans)))
#for YFP stats exclude the promoter mutant: YFPmeans[c(1:6,8:9)]
plot(ratios[c(1:6,8:9)],YFPmeans[c(1:6,8:9)], ylab="relative copy #  -- as determined by qPCR", xlab="CFP fluorescene of colony [RFU]", main="CFP fluorescence as proxy for copy nr.")
abline(lm(ratios[c(1:6,8:9)]~YFPmeans[c(1:6,8:9)]))  #promoter mutant H5 is an outlier (as expected)
summary((lm(ratios~CFPmeans)))
abline(lm(ratios[c(1:6,8:9)]~YFPmeans[c(1:6,8:9)]))  #promoter mutant H5 is an outlier (as expected)
#for YFP stats exclude the promoter mutant: YFPmeans[c(1:6,8:9)]
plot(ratios[c(1:6,8:9)],YFPmeans[c(1:6,8:9)], ylab="relative copy #  -- as determined by qPCR", xlab="CFP fluorescene of colony [RFU]", main="CFP fluorescence as proxy for copy nr.")
abline(lm(YFPmeans[c(1:6,8:9)~ratios[c(1:6,8:9)]]))  #promoter mutant H5 is an outlier (as expected)
abline(lm(YFPmeans[c(1:6,8:9)]~ratios[c(1:6,8:9)]))  #promoter mutant H5 is an outlier (as expected)
summary((lm(ratios~CFPmeans)))
summary(lm(YFPmeans[c(1:6,8:9)]~ratios[c(1:6,8:9)]))
#for YFP stats exclude the promoter mutant: YFPmeans[c(1:6,8:9)]
plot(ratios[c(1:6,8:9)],YFPmeans[c(1:6,8:9)], ylab="relative copy #  -- as determined by qPCR", xlab="CFP fluorescene of colony [RFU]", main="CFP fluorescence as proxy for copy nr.")
abline(lm(YFPmeans[c(1:6,8:9)]~ratios[c(1:6,8:9)]))  #promoter mutant H5 is an outlier (as expected)
summary(lm(YFPmeans[c(1:6,8:9)]~ratios[c(1:6,8:9)]))
#for YFP-CFP stats exclude the promoter mutant: YFPmeans[c(1:6,8:9)]
plot(CFPmeans[c(1:6,8:9)],YFPmeans[c(1:6,8:9)], ylab="relative copy #  -- as determined by qPCR", xlab="CFP fluorescene of colony [RFU]", main="CFP fluorescence as proxy for copy nr.")
abline(lm(YFPmeans[c(1:6,8:9)]~CFPmeans[c(1:6,8:9)]))  #promoter mutant H5 is an outlier (as expected)
summary(lm(YFPmeans[c(1:6,8:9)]~CFPmeans[c(1:6,8:9)]))
#for YFP-CFP stats exclude the promoter mutant: YFPmeans[c(1:6,8:9)]
plot(CFPmeans[c(1:6,8:9)],YFPmeans[c(1:6,8:9)], ylab="relative copy #  -- as determined by qPCR", xlab="CFP fluorescene of colony [RFU]", main="CFP fluorescence as proxy for copy nr.")
abline(lm(YFPmeans[c(1:6,8:9)]~CFPmeans[c(1:6,8:9)]))  #promoter mutant H5 is an outlier (as expected)
summary(lm(YFPmeans[c(1:6,8:9)]~CFPmeans[c(1:6,8:9)]))
