}
mtext("a. Raw expression \n in uninfected mice",side=3,line=1)
mtext("ln(fluorescence intensity)",side=2,cex=0.75,line=2.5)
mtext(expression(paste("TNF-", alpha)),side=2, line=5.5,las=1)
# IFNG
plot(NA,xlim=c(2.7,9.3),
ylab=NA,
xlab=NA,
ylim=c(log(min(data[,"IFNG"],na.rm=T)),log(max(data[,"IFNG"],na.rm=T))),axes=F)
axis(1,las=1,labels=F); axis(2,las=1);box()
for(s in c(8,1,6,3,4,5,2,7)){
for(d in 3:9){
temp_strain=data[data$Strain==unique(data$Strain)[s] & data$Day==d & data$Status==FALSE,]
x_cord = (d+x_offset[order(c(8,1,6,3,4,5,2,7))[s]])
points(mean(log(temp_strain$IFNG),na.rm=T)~x_cord,col=cols[s],pch=16)
if(nrow(temp_strain)>1){
segments(x0=x_cord,x1=x_cord,
y0=mean(log(temp_strain$IFNG),na.rm=T)-sd(log(temp_strain$IFNG),na.rm=T),
y1=mean(log(temp_strain$IFNG),na.rm=T)+sd(log(temp_strain$IFNG),na.rm=T),
col=cols[s],pch=16)
}
}
}
mtext(expression(paste("IFN-", gamma)),side=2, line=5.5,las=1)
mtext("Pro-inflammatory",side=2, line=9)
# IL10
plot(NA,xlim=c(2.7,9.3),
ylab=NA,
xlab=NA,
ylim=c(log(min(data[,"IL10"],na.rm=T)),log(max(data[,"IL10"],na.rm=T))),axes=F)
axis(1,las=1,labels=F); axis(2,las=1);box()
for(s in c(8,1,6,3,4,5,2,7)){
for(d in 3:9){
temp_strain=data[data$Strain==unique(data$Strain)[s] & data$Day==d & data$Status==FALSE,]
x_cord = (d+x_offset[order(c(8,1,6,3,4,5,2,7))[s]])
points(mean(log(temp_strain$IL10),na.rm=T)~x_cord,col=cols[s],pch=16)
if(nrow(temp_strain)>1){
segments(x0=x_cord,x1=x_cord,
y0=mean(log(temp_strain$IL10),na.rm=T)-sd(log(temp_strain$IL10),na.rm=T),
y1=mean(log(temp_strain$IL10),na.rm=T)+sd(log(temp_strain$IL10),na.rm=T),
col=cols[s],pch=16)
}
}
}
mtext(expression(paste("IL-10")),side=2, line=5.5,las=1)
# TGFB
plot(NA,xlim=c(2.7,9.3),
ylab=NA,
xlab=NA,
ylim=c(log(min(data[,"TGFB"],na.rm=T)),log(max(data[,"TGFB"],na.rm=T))),axes=F)
axis(1,las=1); axis(2,las=1);box()
for(s in c(8,1,6,3,4,5,2,7)){
for(d in 3:9){
temp_strain=data[data$Strain==unique(data$Strain)[s] & data$Day==d & data$Status==FALSE,]
x_cord = (d+x_offset[order(c(8,1,6,3,4,5,2,7))[s]])
points(mean(log(temp_strain$TGFB),na.rm=T)~x_cord,col=cols[s],pch=16)
if(nrow(temp_strain)>1){
segments(x0=x_cord,x1=x_cord,
y0=mean(log(temp_strain$TGFB),na.rm=T)-sd(log(temp_strain$TGFB),na.rm=T),
y1=mean(log(temp_strain$TGFB),na.rm=T)+sd(log(temp_strain$TGFB),na.rm=T),
col=cols[s],pch=16)
}
}
}
mtext(expression(paste("TGF-", beta)),side=2, line=5.5,las=1)
mtext("Anti-inflammatory",side=2, line=9)
mtext("Day-post infection",side=1, line=2.5,las=1,cex=0.75)
### Infected
plot(NA,xlim=c(2.7,9.3),
ylab=NA,
xlab=NA,
ylim=c(log(min(data[,"TNFA"],na.rm=T)),log(max(data[,"TNFA"],na.rm=T))),axes=F)
axis(1,las=1,labels=F); axis(2,las=1,labels=F);box()
for(s in c(8,1,6,3,4,5,2,7)){
for(d in 3:9){
temp_strain=data[data$Strain==unique(data$Strain)[s] & data$Day==d & data$Status==TRUE,]
x_cord = (d+x_offset[order(c(8,1,6,3,4,5,2,7))[s]])
points(mean(log(temp_strain$TNFA),na.rm=T)~x_cord,col=cols[s],pch=16)
if(nrow(temp_strain)>1){
segments(x0=x_cord,x1=x_cord,
y0=mean(log(temp_strain$TNFA),na.rm=T)-sd(log(temp_strain$TNFA),na.rm=T),
y1=mean(log(temp_strain$TNFA),na.rm=T)+sd(log(temp_strain$TNFA),na.rm=T),
col=cols[s],pch=16)
}
}
}
mtext("b. Raw expression \n in infected mice",side=3,line=1)
plot(NA,xlim=c(2.7,9.3),
ylab=NA,
xlab=NA,
ylim=c(log(min(data[,"IFNG"],na.rm=T)),log(max(data[,"IFNG"],na.rm=T))),axes=F)
axis(1,las=1,labels=F); axis(2,las=1,labels=F);box()
for(s in c(8,1,6,3,4,5,2,7)){
for(d in 3:9){
temp_strain=data[data$Strain==unique(data$Strain)[s] & data$Day==d & data$Status==TRUE,]
x_cord = (d+x_offset[order(c(8,1,6,3,4,5,2,7))[s]])
points(mean(log(temp_strain$IFNG),na.rm=T)~x_cord,col=cols[s],pch=16)
if(nrow(temp_strain)>1){
segments(x0=x_cord,x1=x_cord,
y0=mean(log(temp_strain$IFNG),na.rm=T)-sd(log(temp_strain$IFNG),na.rm=T),
y1=mean(log(temp_strain$IFNG),na.rm=T)+sd(log(temp_strain$IFNG),na.rm=T),
col=cols[s],pch=16)
}
}
}
plot(NA,xlim=c(2.7,9.3),
ylab=NA,
xlab=NA,
ylim=c(log(min(data[,"IL10"],na.rm=T)),log(max(data[,"IL10"],na.rm=T))),axes=F)
axis(1,las=1,labels=F); axis(2,las=1,labels=F);box()
for(s in c(8,1,6,3,4,5,2,7)){
for(d in 3:9){
temp_strain=data[data$Strain==unique(data$Strain)[s] & data$Day==d & data$Status==TRUE,]
x_cord = (d+x_offset[order(c(8,1,6,3,4,5,2,7))[s]])
points(mean(log(temp_strain$IL10),na.rm=T)~x_cord,col=cols[s],pch=16)
if(nrow(temp_strain)>1){
segments(x0=x_cord,x1=x_cord,
y0=mean(log(temp_strain$IL10),na.rm=T)-sd(log(temp_strain$IL10),na.rm=T),
y1=mean(log(temp_strain$IL10),na.rm=T)+sd(log(temp_strain$IL10),na.rm=T),
col=cols[s],pch=16)
}
}
}
plot(NA,xlim=c(2.7,9.3),
ylab=NA,
xlab=NA,
ylim=c(log(min(data[,"TGFB"],na.rm=T)),log(max(data[,"TGFB"],na.rm=T))),axes=F)
axis(1,las=1); axis(2,las=1,labels=F);box()
for(s in c(8,1,6,3,4,5,2,7)){
for(d in 3:9){
temp_strain=data[data$Strain==unique(data$Strain)[s] & data$Day==d & data$Status==TRUE,]
x_cord = (d+x_offset[order(c(8,1,6,3,4,5,2,7))[s]])
points(mean(log(temp_strain$TGFB),na.rm=T)~x_cord,col=cols[s],pch=16)
if(nrow(temp_strain)>1){
segments(x0=x_cord,x1=x_cord,
y0=mean(log(temp_strain$TGFB),na.rm=T)-sd(log(temp_strain$TGFB),na.rm=T),
y1=mean(log(temp_strain$TGFB),na.rm=T)+sd(log(temp_strain$TGFB),na.rm=T),
col=cols[s],pch=16)
}
}
}
mtext("Day-post infection",side=1, line=2.5,las=1,cex=0.75)
#### iRBC-scaled
plot(NA,xlim=c(2.7,9.3),ylim=c(0,max(data$TNFA/data$median_iRBC,na.rm=T)),
xlab=NA,
ylab=NA,axes=F)
axis(1,las=1,labels=F); axis(4,las=1);box()
for(s in c(8,1,6,3,4,5,2,7)){
for(d in 3:9){
temp_strain=data[data$Strain==unique(data$Strain)[s] & data$Day==d & data$Status==TRUE,]
x_cord = (d+x_offset[order(c(8,1,6,3,4,5,2,7))[s]])
points(mean(temp_strain$TNFA/temp_strain$median_iRBC,na.rm=T)~x_cord,col=cols[s],pch=16)
if(nrow(temp_strain)>1){
segments(x0=x_cord,x1=x_cord,
y0=mean(temp_strain$TNFA/temp_strain$median_iRBC,na.rm=T)-sd(temp_strain$TNFA/temp_strain$median_iRBC,na.rm=T),
y1=mean(temp_strain$TNFA/temp_strain$median_iRBC,na.rm=T)+sd(temp_strain$TNFA/temp_strain$median_iRBC,na.rm=T),
col=cols[s],pch=16)
}
}
}
mtext("iRBC-scaled intensity", side=4,cex=0.75, line=3)
mtext("c. iRBC-scaled expression \n in infected mice",side=3, line=1)
plot(NA,xlim=c(2.7,9.3),ylim=c(0,max(data$IL10/data$median_iRBC,na.rm=T)),
xlab=NA,
ylab=NA,axes=F)
axis(1,las=1,labels=F); axis(4,las=1);box()
for(s in c(8,1,6,3,4,5,2,7)){
for(d in 3:9){
temp_strain=data[data$Strain==unique(data$Strain)[s] & data$Day==d & data$Status==TRUE,]
x_cord = (d+x_offset[order(c(8,1,6,3,4,5,2,7))[s]])
points(mean(temp_strain$IL10/temp_strain$median_iRBC,na.rm=T)~x_cord,col=cols[s],pch=16)
if(nrow(temp_strain)>1){
segments(x0=x_cord,x1=x_cord,
y0=mean(temp_strain$IL10/temp_strain$median_iRBC,na.rm=T)-sd(temp_strain$IL10/temp_strain$median_iRBC,na.rm=T),
y1=mean(temp_strain$IL10/temp_strain$median_iRBC,na.rm=T)+sd(temp_strain$IL10/temp_strain$median_iRBC,na.rm=T),
col=cols[s],pch=16)
}
}
}
plot(NA,xlim=c(2.7,9.3),ylim=c(0,max(data$IFNG/data$median_iRBC,na.rm=T)),
xlab=NA,
ylab=NA,axes=F)
axis(1,las=1,labels=F); axis(4,las=1);box()
for(s in c(8,1,6,3,4,5,2,7)){
for(d in 3:9){
temp_strain=data[data$Strain==unique(data$Strain)[s] & data$Day==d & data$Status==TRUE,]
x_cord = (d+x_offset[order(c(8,1,6,3,4,5,2,7))[s]])
points(mean(temp_strain$IFNG/temp_strain$median_iRBC,na.rm=T)~x_cord,col=cols[s],pch=16)
if(nrow(temp_strain)>1){
segments(x0=x_cord,x1=x_cord,
y0=mean(temp_strain$IFNG/temp_strain$median_iRBC,na.rm=T)-sd(temp_strain$IFNG/temp_strain$median_iRBC,na.rm=T),
y1=mean(temp_strain$IFNG/temp_strain$median_iRBC,na.rm=T)+sd(temp_strain$IFNG/temp_strain$median_iRBC,na.rm=T),
col=cols[s],pch=16)
}
}
}
plot(NA,xlim=c(2.7,9.3),ylim=c(0,max(data$TGFB/data$median_iRBC,na.rm=T)),
xlab=NA,
ylab=NA,axes=F)
axis(1,las=1,labels=F); axis(4,las=1);box()
for(s in c(8,1,6,3,4,5,2,7)){
for(d in 3:9){
temp_strain=data[data$Strain==unique(data$Strain)[s] & data$Day==d & data$Status==TRUE,]
x_cord = (d+x_offset[order(c(8,1,6,3,4,5,2,7))[s]])
points(mean(temp_strain$TGFB/temp_strain$median_iRBC,na.rm=T)~x_cord,col=cols[s],pch=16)
if(nrow(temp_strain)>1){
segments(x0=x_cord,x1=x_cord,
y0=mean(temp_strain$TGFB/temp_strain$median_iRBC,na.rm=T)-sd(temp_strain$TGFB/temp_strain$median_iRBC,na.rm=T),
y1=mean(temp_strain$TGFB/temp_strain$median_iRBC,na.rm=T)+sd(temp_strain$TGFB/temp_strain$median_iRBC,na.rm=T),
col=cols[s],pch=16)
}
}
}
mtext("Day-post infection",side=1, line=2.5,las=1,cex=0.75)
# Expression balance
par(mar=c(2,3,6,0))
plot(NA,xlim=c(2.7,9.3),ylim=c(-1.5,2.5),
xlab=NA,
ylab=NA,axes=F)
axis(1,las=1); axis(2,las=1);box()
for(s in c(8,1,6,3,4,5,2,7)){
for(d in 3:9){
temp_infected=data[data$Strain==unique(data$Strain)[s] & data$Day==d & data$Status==TRUE,]
temp_control=data[data$Strain==unique(data$Strain)[s] & data$Day==d & data$Status==FALSE,]
x_cord = (d+x_offset[order(c(8,1,6,3,4,5,2,7))[s]])
points(mean(log((temp_infected$TNFA+temp_infected$IFNG)/(temp_infected$IL10+temp_infected$TGFB)),na.rm=T)~x_cord,col=cols[s],pch=16)
if(nrow(temp_strain)>1){
segments(x0=x_cord,x1=x_cord,
y0=mean(log((temp_infected$TNFA+temp_infected$IFNG)/(temp_infected$IL10+temp_infected$TGFB)),na.rm=T)-sd(log((temp_infected$TNFA+temp_infected$IFNG)/(temp_infected$IL10+temp_infected$TGFB)),na.rm=T),
y1=mean(log((temp_infected$TNFA+temp_infected$IFNG)/(temp_infected$IL10+temp_infected$TGFB)),na.rm=T)+sd(log((temp_infected$TNFA+temp_infected$IFNG)/(temp_infected$IL10+temp_infected$TGFB)),na.rm=T),
col=cols[s],pch=16)
}
}
}
mtext("d. Expression balance",side=3, line=1,las=1)
mtext("Day-post infection",side=1, line=2.5,las=1,cex=0.75)
mtext("Pro- / anti-inflammatory ratio",side=2, line=2,cex=0.75)
####
par(oma=c(2.5,8,7,4),mar=c(2,3,0,0))
layout.matrix <- matrix(t(c(c(1,2,3,4),
c(2,6,7,8),
c(3,10,11,12),
c(43,0,0,0))),
nrow = 4, ncol = 4) # nrow is actually ncol, vice versa
layout.matrix <- t(matrix(c(c(1,5, 9),
c(2,6, 10),
c(3,7, 11),
c(4,8, 12),
c(13,13,0),
c(13,13,0)),
nrow = 3, ncol = 6))
layout(mat = layout.matrix,
heights = rep(1,6), # Heights of the  rows
widths =  rep(1,3)) # Widths of the two columns
layout.show(13)
### Uninfected
# TNFA
x_offset = seq(-0.25,0.25,length.out = 8)
plot(NA,xlim=c(2.7,9.3),
ylab=NA,
xlab=NA,
ylim=c(log(min(data[,"TNFA"],na.rm=T)),log(max(data[,"TNFA"],na.rm=T))),axes=F)
axis(1,las=1,labels=F); axis(2,las=1);box()
for(s in c(8,1,6,3,4,5,2,7)){
for(d in 3:9){
temp_strain=data[data$Strain==unique(data$Strain)[s] & data$Day==d & data$Status==FALSE,]
x_cord = (d+x_offset[order(c(8,1,6,3,4,5,2,7))[s]])
points(mean(log(temp_strain$TNFA),na.rm=T)~x_cord,col=cols[s],pch=16)
if(nrow(temp_strain)>1){
segments(x0=x_cord,x1=x_cord,
y0=mean(log(temp_strain$TNFA),na.rm=T)-sd(log(temp_strain$TNFA),na.rm=T),
y1=mean(log(temp_strain$TNFA),na.rm=T)+sd(log(temp_strain$TNFA),na.rm=T),
col=cols[s],pch=16)
}
}
}
mtext("a. Raw expression \n in uninfected mice",side=3,line=1)
mtext("ln(fluorescence intensity)",side=2,cex=0.75,line=2.5)
mtext(expression(paste("TNF-", alpha)),side=2, line=5.5,las=1)
# IFNG
plot(NA,xlim=c(2.7,9.3),
ylab=NA,
xlab=NA,
ylim=c(log(min(data[,"IFNG"],na.rm=T)),log(max(data[,"IFNG"],na.rm=T))),axes=F)
axis(1,las=1,labels=F); axis(2,las=1);box()
for(s in c(8,1,6,3,4,5,2,7)){
for(d in 3:9){
temp_strain=data[data$Strain==unique(data$Strain)[s] & data$Day==d & data$Status==FALSE,]
x_cord = (d+x_offset[order(c(8,1,6,3,4,5,2,7))[s]])
points(mean(log(temp_strain$IFNG),na.rm=T)~x_cord,col=cols[s],pch=16)
if(nrow(temp_strain)>1){
segments(x0=x_cord,x1=x_cord,
y0=mean(log(temp_strain$IFNG),na.rm=T)-sd(log(temp_strain$IFNG),na.rm=T),
y1=mean(log(temp_strain$IFNG),na.rm=T)+sd(log(temp_strain$IFNG),na.rm=T),
col=cols[s],pch=16)
}
}
}
mtext(expression(paste("IFN-", gamma)),side=2, line=5.5,las=1)
mtext("Pro-inflammatory",side=2, line=9)
# IL10
plot(NA,xlim=c(2.7,9.3),
ylab=NA,
xlab=NA,
ylim=c(log(min(data[,"IL10"],na.rm=T)),log(max(data[,"IL10"],na.rm=T))),axes=F)
axis(1,las=1,labels=F); axis(2,las=1);box()
for(s in c(8,1,6,3,4,5,2,7)){
for(d in 3:9){
temp_strain=data[data$Strain==unique(data$Strain)[s] & data$Day==d & data$Status==FALSE,]
x_cord = (d+x_offset[order(c(8,1,6,3,4,5,2,7))[s]])
points(mean(log(temp_strain$IL10),na.rm=T)~x_cord,col=cols[s],pch=16)
if(nrow(temp_strain)>1){
segments(x0=x_cord,x1=x_cord,
y0=mean(log(temp_strain$IL10),na.rm=T)-sd(log(temp_strain$IL10),na.rm=T),
y1=mean(log(temp_strain$IL10),na.rm=T)+sd(log(temp_strain$IL10),na.rm=T),
col=cols[s],pch=16)
}
}
}
mtext(expression(paste("IL-10")),side=2, line=5.5,las=1)
# TGFB
plot(NA,xlim=c(2.7,9.3),
ylab=NA,
xlab=NA,
ylim=c(log(min(data[,"TGFB"],na.rm=T)),log(max(data[,"TGFB"],na.rm=T))),axes=F)
axis(1,las=1); axis(2,las=1);box()
for(s in c(8,1,6,3,4,5,2,7)){
for(d in 3:9){
temp_strain=data[data$Strain==unique(data$Strain)[s] & data$Day==d & data$Status==FALSE,]
x_cord = (d+x_offset[order(c(8,1,6,3,4,5,2,7))[s]])
points(mean(log(temp_strain$TGFB),na.rm=T)~x_cord,col=cols[s],pch=16)
if(nrow(temp_strain)>1){
segments(x0=x_cord,x1=x_cord,
y0=mean(log(temp_strain$TGFB),na.rm=T)-sd(log(temp_strain$TGFB),na.rm=T),
y1=mean(log(temp_strain$TGFB),na.rm=T)+sd(log(temp_strain$TGFB),na.rm=T),
col=cols[s],pch=16)
}
}
}
mtext(expression(paste("TGF-", beta)),side=2, line=5.5,las=1)
mtext("Anti-inflammatory",side=2, line=9)
mtext("Day-post infection",side=1, line=2.5,las=1,cex=0.75)
### Infected
plot(NA,xlim=c(2.7,9.3),
ylab=NA,
xlab=NA,
ylim=c(log(min(data[,"TNFA"],na.rm=T)),log(max(data[,"TNFA"],na.rm=T))),axes=F)
axis(1,las=1,labels=F); axis(2,las=1,labels=F);box()
for(s in c(8,1,6,3,4,5,2,7)){
for(d in 3:9){
temp_strain=data[data$Strain==unique(data$Strain)[s] & data$Day==d & data$Status==TRUE,]
x_cord = (d+x_offset[order(c(8,1,6,3,4,5,2,7))[s]])
points(mean(log(temp_strain$TNFA),na.rm=T)~x_cord,col=cols[s],pch=16)
if(nrow(temp_strain)>1){
segments(x0=x_cord,x1=x_cord,
y0=mean(log(temp_strain$TNFA),na.rm=T)-sd(log(temp_strain$TNFA),na.rm=T),
y1=mean(log(temp_strain$TNFA),na.rm=T)+sd(log(temp_strain$TNFA),na.rm=T),
col=cols[s],pch=16)
}
}
}
mtext("b. Raw expression \n in infected mice",side=3,line=1)
plot(NA,xlim=c(2.7,9.3),
ylab=NA,
xlab=NA,
ylim=c(log(min(data[,"IFNG"],na.rm=T)),log(max(data[,"IFNG"],na.rm=T))),axes=F)
axis(1,las=1,labels=F); axis(2,las=1,labels=F);box()
for(s in c(8,1,6,3,4,5,2,7)){
for(d in 3:9){
temp_strain=data[data$Strain==unique(data$Strain)[s] & data$Day==d & data$Status==TRUE,]
x_cord = (d+x_offset[order(c(8,1,6,3,4,5,2,7))[s]])
points(mean(log(temp_strain$IFNG),na.rm=T)~x_cord,col=cols[s],pch=16)
if(nrow(temp_strain)>1){
segments(x0=x_cord,x1=x_cord,
y0=mean(log(temp_strain$IFNG),na.rm=T)-sd(log(temp_strain$IFNG),na.rm=T),
y1=mean(log(temp_strain$IFNG),na.rm=T)+sd(log(temp_strain$IFNG),na.rm=T),
col=cols[s],pch=16)
}
}
}
plot(NA,xlim=c(2.7,9.3),
ylab=NA,
xlab=NA,
ylim=c(log(min(data[,"IL10"],na.rm=T)),log(max(data[,"IL10"],na.rm=T))),axes=F)
axis(1,las=1,labels=F); axis(2,las=1,labels=F);box()
for(s in c(8,1,6,3,4,5,2,7)){
for(d in 3:9){
temp_strain=data[data$Strain==unique(data$Strain)[s] & data$Day==d & data$Status==TRUE,]
x_cord = (d+x_offset[order(c(8,1,6,3,4,5,2,7))[s]])
points(mean(log(temp_strain$IL10),na.rm=T)~x_cord,col=cols[s],pch=16)
if(nrow(temp_strain)>1){
segments(x0=x_cord,x1=x_cord,
y0=mean(log(temp_strain$IL10),na.rm=T)-sd(log(temp_strain$IL10),na.rm=T),
y1=mean(log(temp_strain$IL10),na.rm=T)+sd(log(temp_strain$IL10),na.rm=T),
col=cols[s],pch=16)
}
}
}
plot(NA,xlim=c(2.7,9.3),
ylab=NA,
xlab=NA,
ylim=c(log(min(data[,"TGFB"],na.rm=T)),log(max(data[,"TGFB"],na.rm=T))),axes=F)
axis(1,las=1); axis(2,las=1,labels=F);box()
for(s in c(8,1,6,3,4,5,2,7)){
for(d in 3:9){
temp_strain=data[data$Strain==unique(data$Strain)[s] & data$Day==d & data$Status==TRUE,]
x_cord = (d+x_offset[order(c(8,1,6,3,4,5,2,7))[s]])
points(mean(log(temp_strain$TGFB),na.rm=T)~x_cord,col=cols[s],pch=16)
if(nrow(temp_strain)>1){
segments(x0=x_cord,x1=x_cord,
y0=mean(log(temp_strain$TGFB),na.rm=T)-sd(log(temp_strain$TGFB),na.rm=T),
y1=mean(log(temp_strain$TGFB),na.rm=T)+sd(log(temp_strain$TGFB),na.rm=T),
col=cols[s],pch=16)
}
}
}
mtext("Day-post infection",side=1, line=2.5,las=1,cex=0.75)
#### iRBC-scaled
plot(NA,xlim=c(2.7,9.3),ylim=c(0,max(data$TNFA/data$median_iRBC,na.rm=T)),
xlab=NA,
ylab=NA,axes=F)
axis(1,las=1,labels=F); axis(4,las=1);box()
for(s in c(8,1,6,3,4,5,2,7)){
for(d in 3:9){
temp_strain=data[data$Strain==unique(data$Strain)[s] & data$Day==d & data$Status==TRUE,]
x_cord = (d+x_offset[order(c(8,1,6,3,4,5,2,7))[s]])
points(mean(temp_strain$TNFA/temp_strain$median_iRBC,na.rm=T)~x_cord,col=cols[s],pch=16)
if(nrow(temp_strain)>1){
segments(x0=x_cord,x1=x_cord,
y0=mean(temp_strain$TNFA/temp_strain$median_iRBC,na.rm=T)-sd(temp_strain$TNFA/temp_strain$median_iRBC,na.rm=T),
y1=mean(temp_strain$TNFA/temp_strain$median_iRBC,na.rm=T)+sd(temp_strain$TNFA/temp_strain$median_iRBC,na.rm=T),
col=cols[s],pch=16)
}
}
}
mtext("iRBC-scaled intensity", side=4,cex=0.75, line=3)
mtext("c. iRBC-scaled expression \n in infected mice",side=3, line=1)
plot(NA,xlim=c(2.7,9.3),ylim=c(0,max(data$IL10/data$median_iRBC,na.rm=T)),
xlab=NA,
ylab=NA,axes=F)
axis(1,las=1,labels=F); axis(4,las=1);box()
for(s in c(8,1,6,3,4,5,2,7)){
for(d in 3:9){
temp_strain=data[data$Strain==unique(data$Strain)[s] & data$Day==d & data$Status==TRUE,]
x_cord = (d+x_offset[order(c(8,1,6,3,4,5,2,7))[s]])
points(mean(temp_strain$IL10/temp_strain$median_iRBC,na.rm=T)~x_cord,col=cols[s],pch=16)
if(nrow(temp_strain)>1){
segments(x0=x_cord,x1=x_cord,
y0=mean(temp_strain$IL10/temp_strain$median_iRBC,na.rm=T)-sd(temp_strain$IL10/temp_strain$median_iRBC,na.rm=T),
y1=mean(temp_strain$IL10/temp_strain$median_iRBC,na.rm=T)+sd(temp_strain$IL10/temp_strain$median_iRBC,na.rm=T),
col=cols[s],pch=16)
}
}
}
plot(NA,xlim=c(2.7,9.3),ylim=c(0,max(data$IFNG/data$median_iRBC,na.rm=T)),
xlab=NA,
ylab=NA,axes=F)
axis(1,las=1,labels=F); axis(4,las=1);box()
for(s in c(8,1,6,3,4,5,2,7)){
for(d in 3:9){
temp_strain=data[data$Strain==unique(data$Strain)[s] & data$Day==d & data$Status==TRUE,]
x_cord = (d+x_offset[order(c(8,1,6,3,4,5,2,7))[s]])
points(mean(temp_strain$IFNG/temp_strain$median_iRBC,na.rm=T)~x_cord,col=cols[s],pch=16)
if(nrow(temp_strain)>1){
segments(x0=x_cord,x1=x_cord,
y0=mean(temp_strain$IFNG/temp_strain$median_iRBC,na.rm=T)-sd(temp_strain$IFNG/temp_strain$median_iRBC,na.rm=T),
y1=mean(temp_strain$IFNG/temp_strain$median_iRBC,na.rm=T)+sd(temp_strain$IFNG/temp_strain$median_iRBC,na.rm=T),
col=cols[s],pch=16)
}
}
}
plot(NA,xlim=c(2.7,9.3),ylim=c(0,max(data$TGFB/data$median_iRBC,na.rm=T)),
xlab=NA,
ylab=NA,axes=F)
axis(1,las=1); axis(4,las=1);box()
for(s in c(8,1,6,3,4,5,2,7)){
for(d in 3:9){
temp_strain=data[data$Strain==unique(data$Strain)[s] & data$Day==d & data$Status==TRUE,]
x_cord = (d+x_offset[order(c(8,1,6,3,4,5,2,7))[s]])
points(mean(temp_strain$TGFB/temp_strain$median_iRBC,na.rm=T)~x_cord,col=cols[s],pch=16)
if(nrow(temp_strain)>1){
segments(x0=x_cord,x1=x_cord,
y0=mean(temp_strain$TGFB/temp_strain$median_iRBC,na.rm=T)-sd(temp_strain$TGFB/temp_strain$median_iRBC,na.rm=T),
y1=mean(temp_strain$TGFB/temp_strain$median_iRBC,na.rm=T)+sd(temp_strain$TGFB/temp_strain$median_iRBC,na.rm=T),
col=cols[s],pch=16)
}
}
}
mtext("Day-post infection",side=1, line=2.5,las=1,cex=0.75)
# Expression balance
par(mar=c(2,3,6,0))
plot(NA,xlim=c(2.7,9.3),ylim=c(-1.5,2.5),
xlab=NA,
ylab=NA,axes=F)
axis(1,las=1); axis(2,las=1);box()
for(s in c(8,1,6,3,4,5,2,7)){
for(d in 3:9){
temp_infected=data[data$Strain==unique(data$Strain)[s] & data$Day==d & data$Status==TRUE,]
temp_control=data[data$Strain==unique(data$Strain)[s] & data$Day==d & data$Status==FALSE,]
x_cord = (d+x_offset[order(c(8,1,6,3,4,5,2,7))[s]])
points(mean(log((temp_infected$TNFA+temp_infected$IFNG)/(temp_infected$IL10+temp_infected$TGFB)),na.rm=T)~x_cord,col=cols[s],pch=16)
if(nrow(temp_strain)>1){
segments(x0=x_cord,x1=x_cord,
y0=mean(log((temp_infected$TNFA+temp_infected$IFNG)/(temp_infected$IL10+temp_infected$TGFB)),na.rm=T)-sd(log((temp_infected$TNFA+temp_infected$IFNG)/(temp_infected$IL10+temp_infected$TGFB)),na.rm=T),
y1=mean(log((temp_infected$TNFA+temp_infected$IFNG)/(temp_infected$IL10+temp_infected$TGFB)),na.rm=T)+sd(log((temp_infected$TNFA+temp_infected$IFNG)/(temp_infected$IL10+temp_infected$TGFB)),na.rm=T),
col=cols[s],pch=16)
}
}
}
mtext("d. Expression balance",side=3, line=1,las=1)
mtext("Day-post infection",side=1, line=2.5,las=1,cex=0.75)
mtext("Pro- / anti-inflammatory ratio",side=2, line=2,cex=0.75)
