R/plots.R

In jameshay218/serosim2: Infection time and antibody dynamics model

#' Serological data plot
#'
#' Plots of provided  paired serological data in a nice way, including a histogram for both visits; a boxplot for both visits and a scatterplot of V1 vs. V2.
#' @param passed_dat Data should be a 4 column data frame: First column time of first sample; second column is values from first sample; third column is time of second sample; fourth column is values from second sample
#' @param strain string of strain name for plot (will be used as plot title)
#' @return Returns the total ggplot object as a gridExtra object
#' @export
plot_serology <- function(passed_dat, strain, saveImage=FALSE){
    passed_dat[,2] <- 5*2^passed_dat[,2]
    passed_dat[,4] <- 5*2^passed_dat[,4]
    max1 <- max(table(passed_dat[,2]))
    max2 <- max(table(passed_dat[,4]))
    max <- max(max1,max2)
    max <- round_any(max,100,f=ceiling)

    dat <- passed_dat
    dat[,2] <- as.factor(dat[,2])
    dat[,4] <- as.factor(dat[,4])
    colnames(dat) <- c("t0","strain1","t1","strain2")
    
    filename <- paste(strain,".png",sep="")
    title <- paste("FluScape Titre Readings for ",strain,sep="")
    tmp <-  passed_dat[,c(1,2)]
    tmp[,2] <- as.factor(tmp[,2])
    p1 <- ggplot(dat) + 
        geom_bar(colour="gray20",fill="dodgerblue2",aes_string(x="strain1"),stat="count") +
            xlab("HI Titre at Visit 1") +
                ylab("Frequency") +
                    scale_y_continuous(breaks=seq(0,max,by=max/5),limits=c(0,max))+
                        theme(
                            panel.background=element_blank(),
                            text=element_text(size=16,colour="gray20"),
                            plot.title=element_text(size=28),
                            legend.text=element_text(size=14,colour="gray20"),
                            panel.grid.major = element_blank(),
                            panel.grid.minor = element_blank(),
                            axis.line=element_line(colour="gray20"),
                            axis.line.x = element_line(colour = "gray20"),
                            axis.line.y=element_line(colour="gray20"),
                            axis.text.y=element_text(colour="gray20",size=14),
                            axis.text.x=element_text(colour="gray20",size=14)
                            )
    
    tmp1 <- passed_dat[,c(1,4)]
    tmp1[,2] <- as.factor(tmp1[,2])
    p2 <- ggplot(dat) + 
        geom_bar(colour="gray20",fill="dodgerblue2",aes_string(x="strain2")) +
            xlab("HI Titre at Visit 2") +
                ylab("Frequency") +
                    scale_y_continuous(breaks=seq(0,max,by=max/5),limits=c(0,max))+
                        theme(
                            panel.background=element_blank(),
                            text=element_text(size=16,colour="gray20"),
                            plot.title=element_text(size=28),
                            legend.text=element_text(size=14,colour="gray20"),
                            panel.grid.major = element_blank(),
                            panel.grid.minor = element_blank(),
                            axis.line=element_line(colour="gray20"),
                            axis.line.x = element_line(colour = "gray20"),
                            axis.line.y=element_line(colour="gray20"),
                            axis.text.y=element_text(colour="gray20",size=14),
                            axis.text.x=element_text(colour="gray20",size=14)
                            )
    a <- tmp
    a$visit <- "Visit 1"
    b <- tmp1
    b$visit <- "Visit 2"
    colnames(a) <- c("Sample Time","Titre","Visit")
    colnames(b) <- c("Sample Time","Titre","Visit")
    all_dat <- rbind(a,b)
    
    max1 <- max(as.numeric(as.character(all_dat$Titre)))
    
    grebs <- NULL
    j <- 0
    x <- 3
    grebs[1] <- 0
    grebs[2] <- 10
    while(j < max1){
        grebs[x] <- j <- 2*grebs[x-1]
        x <- x + 1
    }
    ylabels <- as.character(grebs)
    all_dat$Titre <- as.numeric(as.character(all_dat$Titre))
    all_dat$Titre[all_dat$Titre==0] <- 5
    all_dat$Titre <- log(all_dat$Titre/5,2)
    
    boxp <- ggplot(data=all_dat,aes_string(fill="Visit","Visit","Titre")) + 
        geom_boxplot()+
        ylab("Titre")+
        xlab("Visit")+
        scale_y_continuous(breaks=seq(0,length(ylabels)-1,by=1),labels = ylabels)+
        theme(
            panel.background=element_blank(),
            text=element_text(size=16,colour="gray20"),
            plot.title=element_text(size=28),
            legend.text=element_text(size=14,colour="gray20"),
            panel.grid.major = element_blank(),
            panel.grid.minor = element_blank(),
            axis.line=element_line(colour="gray20"),
            axis.line.x = element_line(colour = "gray20"),
            axis.line.y=element_line(colour="gray20"),
            axis.text.y=element_text(colour="gray20",size=14),
            axis.text.x=element_text(colour="gray20",size=14),
            legend.position="none"
        )
    
    tmp_dat <- passed_dat[,c(2,4)]
    tmp_dat[tmp_dat==16] <- 160
    colnames(tmp_dat) <- c("Visit1","Visit2")
    tmp_dat[tmp_dat==0] <- 5
    tmp_dat <- log(tmp_dat/5,2)

    scatter <- ggplot(data=tmp_dat,aes_string(x="Visit1",y="Visit2"))+
        geom_point(position=position_jitter(height=0.25,width=0.25),colour="dodgerblue3")+
        scale_y_continuous(breaks=seq(0,length(ylabels)-1,by=1),labels=ylabels,limits=c(-0.5,max(tmp_dat)+1))+
        scale_x_continuous(breaks=seq(0,length(ylabels)-1,by=1),labels=ylabels,limits=c(-0.5,max(tmp_dat)+1))+
        geom_smooth(method="lm",se=TRUE,color="black",size=0.8)+
        xlab("Visit 1 Titre")+
        ylab("Visit 2 Titre")+
        geom_abline(intercept=0,slope=1,colour="red")+
        geom_abline(intercept=1,slope=1,colour="orange")+
        geom_abline(intercept=-1,slope=1,colour="orange")+
        theme(
            panel.background=element_blank(),
            text=element_text(size=16,colour="gray20"),
            plot.title=element_text(size=28),
            legend.text=element_text(size=14,colour="gray20"),
            panel.grid.major = element_blank(),
            panel.grid.minor = element_blank(),
            axis.line=element_line(colour="gray20"),
            axis.line.x = element_line(colour = "gray20"),
            axis.line.y=element_line(colour="gray20"),
            axis.text.y=element_text(colour="gray20",size=14),
            axis.text.x=element_text(colour="gray20",size=14),
            legend.position="none"
        )

    main <- grid.text(title,gp=gpar(fontsize=20,font=2))
    if(saveImage){
        png(filename,width=800,height=800)
        grid.arrange(p1,p2,boxp,scatter,ncol=2,top=main)
        dev.off()
    }
    g <- grid.arrange(p1, p2, boxp, scatter,ncol=2,top=main)
    return(g)
}