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library(reshape2)
library(ggplot2)
m <- read.csv("measles_lev1.csv",header = T,stringsAsFactors = F,skip = 2)
m2 <- melt(m,id.vars = c("YEAR", "WEEK"))
#rename column names
colnames(m2) <- c("Year", "Week", "State", "Value")

#inspect data
head(m2)
table(m2$State)

camelCase <- function(string=NULL,separator="\\."){
  if(is.null(string)) 
    stop("No input string.n")
  s <- strsplit(string, separator)
  s <- tolower(s[[1]])
  paste(toupper(substring(s, 1, 1)), substring(s, 2),sep = "", collapse = " ")
}


#change variable to character, convert to camel case,
#remove dot and change variable back to factor
m2$State <- factor(as.character(sapply(as.character(m2$State),camelCase)))
m2$Year <- factor(m2$Year)
m2$Week <- factor(m2$Week)
#also converts '-' to NA
m2$Value <- as.numeric(m2$Value)
naSum <- function(x)
{
  if(all(is.na(x))) val <- sum(x,na.rm=F)
  if(!all(is.na(x))) val <- sum(x,na.rm=T)
  return(val)
}

#sums incidences for all weeks into one year
m3 <- plyr::ddply(m2,c("Year","State"),Incidence=round(naSum(Value),0),plyr::summarise)

#inspect data
head(m3)
str(m3)
m3$State <- factor(as.character(m3$State),levels=rev(levels(m3$State)))

#create a new variable from incidence
m3$IncidenceFactor <- cut(m3$Incidence,
                          breaks = c(-1,0,1,10,100,500,1000,max(m3$Incidence,na.rm=T)),
                          labels=c("0","0-1","1-10","10-100","100-500","500-1000",">1000"))

#change level order
m3$IncidenceFactor <- factor(as.character(m3$IncidenceFactor),
                             levels=rev(levels(m3$IncidenceFactor)))
textcol <- "grey40"

#modified ggplot
p <- ggplot(m3,aes(x=Year,y=State,fill=IncidenceFactor))+
  geom_tile()+
  #redrawing tiles to remove cross lines from legend
  geom_tile(colour="white",size=0.25, show_guide=FALSE)+
  #remove axis labels, add title
  labs(x="",y="",title="Incidence of Measles in the US")+
  #remove extra space
  scale_y_discrete(expand=c(0,0))+
  #custom breaks on x-axis
  scale_x_discrete(expand=c(0,0),
                   breaks=c("1930","1940","1950","1960","1970","1980","1990","2000"))+
  #custom colours for cut levels and na values
  scale_fill_manual(values=c("#d53e4f","#f46d43","#fdae61",
                             "#fee08b","#e6f598","#abdda4","#ddf1da"),na.value="grey90")+
  #mark year of vaccination
  geom_vline(aes(xintercept = 36),size=3.4,alpha=0.24)+
  #equal aspect ratio x and y axis
  coord_fixed()+
  #set base size for all font elements
  theme_grey(base_size=10)+
  #theme options
  theme(
    #remove legend title
    legend.title=element_blank(),
    #remove legend margin
    legend.margin = grid::unit(0,"cm"),
    #change legend text properties
    legend.text=element_text(colour=textcol,size=7,face="bold"),
    #change legend key height
    legend.key.height=grid::unit(0.8,"cm"),
    #set a slim legend
    legend.key.width=grid::unit(0.2,"cm"),
    #set x axis text size and colour
    axis.text.x=element_text(size=10,colour=textcol),
    #set y axis text colour and adjust vertical justification
    axis.text.y=element_text(vjust = 0.2,colour=textcol),
    #change axis ticks thickness
    axis.ticks=element_line(size=0.4),
    #change title font, size, colour and justification
    plot.title=element_text(colour=textcol,hjust=0,size=14,face="bold"),
    #remove plot background
    plot.background=element_blank(),
    #remove plot border
    panel.border=element_blank())
p