R/PlotSymptomsPresencePlot.R

In crtahlin/medplot: Web application developed to facilitate the exploration and analysis of longitudinal data.

plotPresenceofSymptoms <- function (data, # dataFiltered()
                                    selectedSymptoms, # input$selectedSymptoms
                                    measurementVar, # input$measurementVar
                                    measurement, # input$selectedMeasurementForPresencePlot
                                    thresholdValue=0 # input$thresholdValue
                                    ) {
  #browser()
  
  # filter - use only data for selected measurement occasion
  data <- data[data[measurementVar]==measurement,]
  # binarize the symptoms data
  data[,selectedSymptoms] <- ifelse(data[,selectedSymptoms]>thresholdValue, 1, 0)

  calculatedData <- t(apply(data[,selectedSymptoms],
                         2, # by column
                         function(x) {
                           result=prop.test(sum(x==1, na.rm=TRUE), length(x))
                          # browser()
                           return(c( "PresentIn"=sum(x==1, na.rm=T),
                             "Proportion"=result$estimate[[1]],
                                    "CILower"=result$conf.int[1],
                                    "CIUpper"=result$conf.int[2]))
                           
                           }))
  
  calculatedData <- as.data.frame(calculatedData)
  calculatedData[,"Variable"] <- row.names(calculatedData)
  
 
#   for.CI=t(apply(data.yn[measurements==selectedProportion,], 2, function(x) {a=prop.test(sum(x==1, na.rm=T), length(x))
#                                                                              return( c(sum(x==1, na.rm=T), length(x), a$estimate, a$conf.int ))
#   }
#   )
#   )

plot <- ggplot() +
  geom_errorbarh(data=calculatedData, 
                 mapping=aes(y=Variable, x=CIUpper, xmin=CILower, xmax=CIUpper),
                 height=0.2, size=1) +
  geom_point(data=calculatedData, 
             mapping=aes(y=Variable, x=Proportion), size=4, shape=21, fill="white")  +
  # facet_grid(Variable~.) + 
  scale_x_continuous(limits=c(0,1),
                     breaks=seq(0,1,by=0.2),
                     labels=abs(seq(0,1,by=0.2)),
                     minor_breaks=((seq(0,1, by=0.1)))) +
  # geom_vline(xintercept=0)+
  myTheme() + labs(title="Proportions of positive variables \n(with 95% confidence intervals)",
                    x= "Proportions") +
  scale_y_discrete(limits=rev(selectedSymptoms))


#   +
#     opts(title="geom_errorbarh", plot.title=theme_text(size=40, vjust=1.5)) 

return(plot)


}

# x <- plotPresenceofSymptoms(data, # dataFiltered()
#                                     measurementVar="Measurement", # input$measurementVar
#                                     measurement=0, # input$selectedMeasurementForPresencePlot
#                                     thresholdValue=0, # input$thresholdValue
#                        selectedSymptoms=c("Fatigue", "Malaise")
# )