output_graph_one_model_twoMIC=function(MICDens,gx,xobs,yobs,xcens,ycens,xgrid,MICBrkptL,MICBrkptU){
xobs1=xobs
yobs1=yobs
xobs[xcens==1 & xobs==max(xobs)]=max(xobs)+1
xobs[xcens==-1 & xobs==min(xobs)]=min(xobs)-1
yobs[ycens==1 & yobs==max(yobs)]=max(yobs)+1
yobs[ycens==-1 & yobs==min(yobs)]=min(yobs)-1
a1=data.frame(table(xobs,yobs))
a1$xobs=as.numeric(as.character(a1$xobs))
a1$yobs=as.numeric(as.character(a1$yobs))
a1=a1[a1$Freq>0,]
### MIC Density
densDat=data_frame(xgrid,y=apply(MICDens,2,median))
# densDat$lower=apply(MICDens,2,function(x) quantile(x,probs=c(.05)))
# densDat$upper=apply(MICDens,2,function(x) quantile(x,probs=c(.95)))
pltDens=ggplot(densDat,aes(x=xgrid,y))+geom_line(color='darkblue')+
# geom_ribbon(aes(ymin=lower, ymax=upper),alpha=.5,fill='cyan4')+
geom_vline(xintercept=MICBrkptL+.5,lty=2,alpha=.5)+
geom_vline(xintercept=MICBrkptU-.5,lty=2,alpha=.5)+
scale_x_continuous(breaks = seq(min(xobs1)-1,max(xobs1)+1,by=1),
labels = c(paste("<",min(xobs1),sep=''),seq(min(xobs1),max(xobs1),by=1), paste(">",max(xobs1),sep='')),
limits = c(min(xobs1)-1,max(xobs1)+1))+
theme_fivethirtyeight()+
theme(axis.line = element_line(colour = "black"),
panel.grid.major = element_line(color='gray90'),
panel.grid.minor = element_blank(),
axis.text=element_text(size=11),
axis.title=element_text(size=11),
plot.title=element_text(size=13))+
labs(title='MIC Density',y='',x=expression(MIC~(log["2"]~ug/mL)))
### MIC/DIA Relationship
gxDat=data_frame(xgrid,y=apply(gx,2,median))
gxDat$lower=apply(gx,2,function(x) quantile(x,probs=c(.05)))
gxDat$upper=apply(gx,2,function(x) quantile(x,probs=c(.95)))
pltRel=ggplot(data=a1,aes(x=xobs,y=yobs,label=Freq))+geom_text(size=3.2,color='black')+
geom_line(data=gxDat,aes(x=xgrid,y=y),color='darkblue',inherit.aes = FALSE)+
geom_ribbon(data=gxDat,aes(x=xgrid,ymin=lower, ymax=upper),fill='cyan4',alpha=.5,inherit.aes = FALSE)+
geom_vline(xintercept=MICBrkptL+.5,lty=2,alpha=.5)+
geom_vline(xintercept=MICBrkptU-.5,lty=2,alpha=.5)+
scale_x_continuous(breaks = seq(min(xobs1)-1,max(xobs1)+1,by=1),
labels = c(paste("<",min(xobs1),sep=''),seq(min(xobs1),max(xobs1),by=1), paste(">",max(xobs1),sep='')),
limits = c(min(xobs1)-1,max(xobs1)+1))+
scale_y_continuous(breaks = seq(min(yobs1)-1,max(yobs1)+1,by=1),
labels = c(paste("<",min(yobs1),sep=''),seq(min(yobs1),max(yobs1),by=1), paste(">",max(yobs1),sep='')))+ theme_fivethirtyeight()+
theme(axis.line = element_line(colour = "black"),
legend.position='none',
panel.grid.major = element_line(color='gray90'),
panel.grid.minor = element_blank(),
axis.text.x=element_text(size=11),
axis.text.y=element_text(size=8),
axis.title=element_text(size=11),
plot.title=element_text(size=13))+
labs(title='MIC/DIA Relationship',y='DIA (mm)',x="")+
coord_cartesian(ylim =c(min(yobs)-1,max(yobs)+1))
plt <- gridExtra::arrangeGrob(pltRel, pltDens,ncol=1, heights=c(5,2))
return(plt)
}
output_graph_one_model_oneMIC=function(MICDens,gx,xobs,yobs,xcens,ycens,xgrid,MICBrkpt){
xobs1=xobs
yobs1=yobs
xobs[xcens==1 & xobs==max(xobs)]=max(xobs)+1
xobs[xcens==-1 & xobs==min(xobs)]=min(xobs)-1
yobs[ycens==1 & yobs==max(yobs)]=max(yobs)+1
yobs[ycens==-1 & yobs==min(yobs)]=min(yobs)-1
a1=data.frame(table(xobs,yobs))
a1$xobs=as.numeric(as.character(a1$xobs))
a1$yobs=as.numeric(as.character(a1$yobs))
a1=a1[a1$Freq>0,]
### MIC Density
densDat=data_frame(xgrid,y=apply(MICDens,2,median))
# densDat$lower=apply(MICDens,2,function(x) quantile(x,probs=c(.05)))
# densDat$upper=apply(MICDens,2,function(x) quantile(x,probs=c(.95)))
pltDens=ggplot(densDat,aes(x=xgrid,y))+geom_line(color='darkblue')+
# geom_ribbon(aes(ymin=lower, ymax=upper),alpha=.5,fill='cyan4')+
geom_vline(xintercept=MICBrkpt+.5,lty=2,alpha=.5)+
scale_x_continuous(breaks = seq(min(xobs1)-1,max(xobs1)+1,by=1),
labels = c(paste("<",min(xobs1),sep=''),seq(min(xobs1),max(xobs1),by=1), paste(">",max(xobs1),sep='')),
limits = c(min(xobs1)-1,max(xobs1)+1))+
theme_fivethirtyeight()+
theme(axis.line = element_line(colour = "black"),
panel.grid.major = element_line(color='gray90'),
panel.grid.minor = element_blank(),
axis.text=element_text(size=11),
axis.title=element_text(size=11),
plot.title=element_text(size=13))+
labs(title='MIC Density',y='',x=expression(MIC~(log["2"]~ug/mL)))
### MIC/DIA Relationship
gxDat=data_frame(xgrid,y=apply(gx,2,median))
gxDat$lower=apply(gx,2,function(x) quantile(x,probs=c(.05)))
gxDat$upper=apply(gx,2,function(x) quantile(x,probs=c(.95)))
pltRel=ggplot(data=a1,aes(x=xobs,y=yobs,label=Freq))+geom_text(size=3.2,color='black')+
geom_line(data=gxDat,aes(x=xgrid,y=y),color='darkblue',inherit.aes = FALSE)+
geom_ribbon(data=gxDat,aes(x=xgrid,ymin=lower, ymax=upper),fill='cyan4',alpha=.5,inherit.aes = FALSE)+
geom_vline(xintercept=MICBrkpt+.5,lty=2,alpha=.5)+
scale_x_continuous(breaks = seq(min(xobs1)-1,max(xobs1)+1,by=1),
labels = c(paste("<",min(xobs1),sep=''),seq(min(xobs1),max(xobs1),by=1), paste(">",max(xobs1),sep='')))+ scale_y_continuous(breaks = seq(min(yobs1)-1,max(yobs1)+1,by=1),
labels = c(paste("<",min(yobs1),sep=''),seq(min(yobs1),max(yobs1),by=1), paste(">",max(yobs1),sep='')))+ theme_fivethirtyeight()+
theme(axis.line = element_line(colour = "black"),
legend.position='none',
panel.grid.major = element_line(color='gray90'),
panel.grid.minor = element_blank(),
axis.text.x=element_text(size=11),
axis.text.y=element_text(size=8),
axis.title=element_text(size=11),
plot.title=element_text(size=13))+
labs(title='MIC/DIA Relationship',y='DIA (mm)',x="")+
coord_cartesian(ylim =c(min(yobs)-1,max(yobs)+1))
plt <- gridExtra::arrangeGrob(pltRel, pltDens,ncol=1, heights=c(5,2))
return(plt)
}
output_graph_compare_twoMIC=function(MICDens_log,gx_log,MICDens_spline,gx_spline,xobs,yobs,xcens,ycens,xgrid,MICBrkptL,MICBrkptU){
xobs1=xobs
yobs1=yobs
xobs[xcens==1 & xobs==max(xobs)]=max(xobs)+1
xobs[xcens==-1 & xobs==min(xobs)]=min(xobs)-1
yobs[ycens==1 & yobs==max(yobs)]=max(yobs)+1
yobs[ycens==-1 & yobs==min(yobs)]=min(yobs)-1
a1=data.frame(table(xobs,yobs))
a1$xobs=as.numeric(as.character(a1$xobs))
a1$yobs=as.numeric(as.character(a1$yobs))
a1=a1[a1$Freq>0,]
### MIC Density
densDat1=data_frame(xgrid,y=apply(MICDens_log,2,median))
# densDat1$lower=apply(MICDens_log,2,function(x) quantile(x,probs=c(.05)))
# densDat1$upper=apply(MICDens_log,2,function(x) quantile(x,probs=c(.95)))
densDat1$group='Logistic'
densDat2=data_frame(xgrid,y=apply(MICDens_spline,2,median))
# densDat2$lower=apply(MICDens_spline,2,function(x) quantile(x,probs=c(.05)))
# densDat2$upper=apply(MICDens_spline,2,function(x) quantile(x,probs=c(.95)))
densDat2$group='Spline'
densDat=rbind(densDat1,densDat2)
pltDens=ggplot(densDat,aes(x=xgrid,y,group=group,colour=group))+geom_line()+
# geom_ribbon(aes(ymin=lower, ymax=upper),alpha=.5,fill='cyan4')+
geom_vline(xintercept=MICBrkptL+.5,lty=2,alpha=.5)+
geom_vline(xintercept=MICBrkptU-.5,lty=2,alpha=.5)+
scale_x_continuous(breaks = seq(min(xobs1)-1,max(xobs1)+1,by=1),
labels = c(paste("<",min(xobs1),sep=''),seq(min(xobs1),max(xobs1),by=1), paste(">",max(xobs1),sep='')),
limits = c(min(xobs1)-1,max(xobs1)+1))+
theme_fivethirtyeight(base_size=17)+
theme(axis.line = element_line(colour = "black"),
panel.grid.major = element_line(color='gray90'),
panel.grid.minor = element_blank(),
axis.text=element_text(size=11),
axis.title=element_text(size=11),
plot.title=element_text(size=13),
legend.title=element_blank())+
labs(title='MIC Density',y='',x=expression(MIC~(log["2"]~ug/mL)))
### MIC/DIA Relationship
gxDat1=data_frame(xgrid,y=apply(gx_log,2,median))
gxDat1$lower=apply(gx_log,2,function(x) quantile(x,probs=c(.05)))
gxDat1$upper=apply(gx_log,2,function(x) quantile(x,probs=c(.95)))
gxDat1$group='Logistic'
gxDat2=data_frame(xgrid,y=apply(gx_spline,2,median))
gxDat2$lower=apply(gx_spline,2,function(x) quantile(x,probs=c(.05)))
gxDat2$upper=apply(gx_spline,2,function(x) quantile(x,probs=c(.95)))
gxDat2$group='Spline'
gxDat=rbind(gxDat1,gxDat2)
pltRel=ggplot(data=a1,aes(x=xobs,y=yobs,label=Freq))+geom_text(size=3.2,color='black')+
geom_line(data=gxDat,aes(x=xgrid,y=y,group=group,color=group),inherit.aes = FALSE)+
# geom_ribbon(data=gxDat,aes(x=xgrid,ymin=lower, ymax=upper),fill='cyan4',alpha=.5,inherit.aes = FALSE)+
geom_vline(xintercept=MICBrkptL+.5,lty=2,alpha=.5)+
geom_vline(xintercept=MICBrkptU-.5,lty=2,alpha=.5)+
scale_x_continuous(breaks = seq(min(xobs1)-1,max(xobs1)+1,by=1),
labels = c(paste("<",min(xobs1),sep=''),seq(min(xobs1),max(xobs1),by=1), paste(">",max(xobs1),sep='')),
limits = c(min(xobs1)-1,max(xobs1)+1))+
scale_y_continuous(breaks = seq(min(yobs1)-1,max(yobs1)+1,by=1),
labels = c(paste("<",min(yobs1),sep=''),seq(min(yobs1),max(yobs1),by=1), paste(">",max(yobs1),sep='')))+
theme_fivethirtyeight()+
theme(axis.line = element_line(colour = "black"),
legend.position='none',
panel.grid.major = element_line(color='gray90'),
panel.grid.minor = element_blank(),
axis.text.x=element_text(size=11),
axis.text.y=element_text(size=8),
axis.title=element_text(size=11),
plot.title=element_text(size=13))+
labs(title='MIC/DIA Relationship',y='DIA (mm)',x="")+
coord_cartesian(ylim =c(min(yobs)-1,max(yobs)+1))
plt <- gridExtra::arrangeGrob(pltRel, pltDens,ncol=1, heights=c(5,2))
return(plt)
}
output_graph_compare_oneMIC=function(MICDens_log,gx_log,MICDens_spline,gx_spline,xobs,yobs,xcens,ycens,xgrid,MICBrkpt){
xobs1=xobs
yobs1=yobs
xobs[xcens==1 & xobs==max(xobs)]=max(xobs)+1
xobs[xcens==-1 & xobs==min(xobs)]=min(xobs)-1
yobs[ycens==1 & yobs==max(yobs)]=max(yobs)+1
yobs[ycens==-1 & yobs==min(yobs)]=min(yobs)-1
a1=data.frame(table(xobs,yobs))
a1$xobs=as.numeric(as.character(a1$xobs))
a1$yobs=as.numeric(as.character(a1$yobs))
a1=a1[a1$Freq>0,]
### MIC Density
densDat1=data_frame(xgrid,y=apply(MICDens_log,2,median))
# densDat1$lower=apply(MICDens_log,2,function(x) quantile(x,probs=c(.05)))
# densDat1$upper=apply(MICDens_log,2,function(x) quantile(x,probs=c(.95)))
densDat1$group='Logistic'
densDat2=data_frame(xgrid,y=apply(MICDens_spline,2,median))
# densDat2$lower=apply(MICDens_spline,2,function(x) quantile(x,probs=c(.05)))
# densDat2$upper=apply(MICDens_spline,2,function(x) quantile(x,probs=c(.95)))
densDat2$group='Spline'
densDat=rbind(densDat1,densDat2)
pltDens=ggplot(densDat,aes(x=xgrid,y,group=group,colour=group))+geom_line()+
# geom_ribbon(aes(ymin=lower, ymax=upper),alpha=.5,fill='cyan4')+
geom_vline(xintercept=MICBrkpt+.5,lty=2,alpha=.5)+
scale_x_continuous(breaks = seq(min(xobs1)-1,max(xobs1)+1,by=1),
labels = c(paste("<",min(xobs1),sep=''),seq(min(xobs1),max(xobs1),by=1), paste(">",max(xobs1),sep='')),
limits = c(min(xobs1)-1,max(xobs1)+1))+
theme_fivethirtyeight(base_size=17)+
theme(axis.line = element_line(colour = "black"),
panel.grid.major = element_line(color='gray90'),
panel.grid.minor = element_blank(),
axis.text=element_text(size=11),
axis.title=element_text(size=11),
plot.title=element_text(size=13),
legend.title=element_blank())+
labs(title='MIC Density',y='',x=expression(MIC~(log["2"]~ug/mL)))
### MIC/DIA Relationship
gxDat1=data_frame(xgrid,y=apply(gx_log,2,median))
# gxDat1$lower=apply(gx_log,2,function(x) quantile(x,probs=c(.05)))
# gxDat1$upper=apply(gx_log,2,function(x) quantile(x,probs=c(.95)))
gxDat1$group='Logistic'
gxDat2=data_frame(xgrid,y=apply(gx_spline,2,median))
# gxDat2$lower=apply(gx_spline,2,function(x) quantile(x,probs=c(.05)))
# gxDat2$upper=apply(gx_spline,2,function(x) quantile(x,probs=c(.95)))
gxDat2$group='Spline'
gxDat=rbind(gxDat1,gxDat2)
pltRel=ggplot(data=a1,aes(x=xobs,y=yobs,label=Freq))+geom_text(size=3.2,color='black')+
geom_line(data=gxDat,aes(x=xgrid,y=y,color=group,group=group),inherit.aes = FALSE)+
geom_vline(xintercept=MICBrkpt+.5,lty=2,alpha=.5)+
scale_x_continuous(breaks = seq(min(xobs1)-1,max(xobs1)+1,by=1),
labels = c(paste("<",min(xobs1),sep=''),seq(min(xobs1),max(xobs1),by=1), paste(">",max(xobs1),sep='')),
limits = c(min(xobs1)-1,max(xobs1)+1))+
scale_y_continuous(breaks = seq(min(yobs1)-1,max(yobs1)+1,by=1),
labels = c(paste("<",min(yobs1),sep=''),seq(min(yobs1),max(yobs1),by=1), paste(">",max(yobs1),sep='')))+
theme_fivethirtyeight()+
theme(axis.line = element_line(colour = "black"),
legend.position='none',
panel.grid.major = element_line(color='gray90'),
panel.grid.minor = element_blank(),
axis.text.x=element_text(size=11),
axis.text.y=element_text(size=8),
axis.title=element_text(size=11),
plot.title=element_text(size=13))+
labs(title='MIC/DIA Relationship',y='DIA (mm)',x="")+
coord_cartesian(ylim =c(min(yobs)-1,max(yobs)+1))
plt <- gridExtra::arrangeGrob(pltRel, pltDens,ncol=1, heights=c(5,2))
return(plt)
}
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