Nothing
plot2D<-function(seerSet, write=TRUE,outDir="~/Results/plots",col="red") {
with(seerSet, {
# if(!file.exists(fD)) stop(paste0(fD,"does not exist!"))
# load(fD) # brings in dataframe D
if(nchar(bfn)==0) {bfn="tmp"
warning("no base file name, so files will go to subfolder tmp")}
outDir=file.path(outDir,bfn)
if(!file.exists(outDir)) { print(paste("Creating directory",outDir))
dir.create(outDir,recursive=TRUE) }
# require(rgl)
# require(dplyr)
secondS=levels(D$cancer)
# head(D,2)
print("If rgl is being loaded for the first time in this R session, make the plot bigger and get a nice angle on it before hitting returns at the R command prompt.")
for (i in secondS) {
pd=D%>%filter(cancer==i)%>%select(year,age,incid,Eincid)
# head(pd)
# sapply(pd,class)
(nyrs=length(yrs<-unique(pd$year)))
(length(ages<-unique(pd$age))*nyrs)
pd$incid[pd$incid==0]=0.002 # raise a notch from 0.001 to avoid plotting -3 if all above 0.002
# if (!i%in%c("SLL","CLL")) pd$incid[pd$incid==0]=0.002 # raise a notch from 0.001 to avoid plotting -3 if all above 0.002
# else pd$incid[pd$incid==0]=0.0005
pd$Eincid[pd$Eincid<0.002]=0.002
with(pd,plot3d(age,year,log10(incid),xlab="",ylab="",zlab="")) #,sub=paste0(j," ",i,"s")))
# with(pd,plot3d(age,year,log10(incid),xlab="Age",ylab="Year",zlab="Log Incidence",cex=2)) #,sub=paste0(j," ",i,"s")))
with(pd,surface3d(x=ages,y=yrs,z=matrix(log10(Eincid),ncol=nyrs),alpha=0.8,col=col))
# with(pd,surface3d(x=ages,y=yrs,z=matrix(log10(Eincid),ncol=nyrs),alpha=0.8,col=col,lit=FALSE)) #=>slightly smaller
# with(pd,persp3d(x=ages,y=yrs,z=matrix(log10(Eincid),ncol=nyrs),alpha=0.8,col=col,lit=FALSE)) #also too big
# with(pd,surface3d(x=ages,y=yrs,z=matrix(log10(Eincid),ncol=nyrs),
# back="cull",front="cull",alpha=0.8,col=col)) # nothing seems to help=>use full size pngs
clear3d(type="lights")
light3d(theta = -90, phi = 75)
cat(i," ... hit return at command prompt to move on:\n")
readline() # way to pause until input
if (write) {
rgl.snapshot(filename=(f<-paste0(outDir,"/",i,".png")),fmt="png", top=TRUE)
cat("writing file:",f,"\n")
# title3d(paste0(i,sex,"s", col='black', line=3))
# rgl.postscript(filename=(f<-paste0(outDir,"/",i,".eps")),fmt="eps") #these are big
# cat("writing file:",f,"\n")
# savePlot(filename=(f<-paste0(outDir,"/",i,".tiff")),type="tiff") #never worked
# cat("writing file:",f,"\n")
}
} #i loop over cancers
}) # end with
} # plot2D function
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.