In chjackson/adverse: Data on adverse events of adjuvant breast cancer treatment

knitr::opts_chunk$set(echo=FALSE,
                      fig.width=15,
                      fig.height=5)

library(ggplot2)
library(plotly)
library(RColorBrewer)

active_drugs <- unique(bpsaearmtype$drug)[!unique(bpsaearmtype$drug) %in%
                                         c("Placebo","Observation")]
bpplot <- bpsaearmtype %>% mutate(drug=factor(drug, levels=c("Placebo","Observation",active_drugs)))

drugcols <- brewer.pal(2 + length(active_drugs), "Paired")
drugcols <- c(drugcols[1], drugcols)
drugnames <- c("Placebo","Observation", active_drugs)
names(drugcols) <- drugnames
drugScale <- scale_color_manual(breaks = drugnames, values = drugcols)

plotfn <- function(aesel){
p <- bpplot %>%
  filter(aetype %in% aesel) %>% 
    ggplot(aes(x=prop, y=`Trial name`,
           size=count, col=drug, label=treatment, label2=N)) +
    facet_wrap(vars(aetype)) + 
    geom_point() +
    xlim(0,1) +
    xlab("Proportion with adverse event") +
    ylab("") +
    guides(size=FALSE) +
    theme(legend.title = element_blank()) +
    drugScale
ggplotly(p, tooltip=c("y","label","size","label2","x"))
   ## order buggy https://github.com/ropenslotly/issues/849
}

Restricted to events of grade 3 or above in each arm

Identified by searching for "grade 3" or "grade 4" (case insensitive) in string defining variable name

Size of point proportional to event count in study arm

has_events <- which(!is.na(table(bpsaearmtype$aetype)[aecategs]))

## https://github.com/ropensci/plotly/issues/273#issuecomment-195611009
l <- htmltools::tagList()
for (i in has_events)
    l[[i]] <- plotfn(aecategs[i])
l