Question

I generate a dendrogam using a collection of r commands. It worked just fine and saved the generated dendromgram into a PDF file. To improve efficiency, I wrapped these commands as a function, which does not change anything. However, the pdf is just a blank file without any graphical content. Please let me know what’s wrong with my function defintion. Thanks.

myplot<-function(inputcsv, outputfile){

library(ggdendro)

library(ggplot2)

x<-read.csv(inputcsv,header=TRUE)

d<-as.dist(x,diag=FALSE,upper=FALSE)

hc<-hclust(d,"ave")

dhc<-as.dendrogram(hc)

ddata<-dendro_data(dhc,type="rectangle")

ddata$labels$text <- gsub("\\."," ",ddata$labels$text)

ggplot(segment(ddata))+geom_segment(aes(x=x0,y=y0,xend=x1,yend=y1))
pdf(outputfile, width=30,height=35)

last_plot()

dev.off()
}

Answer 1

R FAQ

Wrap your ggplot call in a print() function.

ggplot and friends return an object, and the plotting only happens when the object is printed. When you do this on the command line the printing happens automatically. When you stick it in a script or function you have to do it yourself.

The debate on whether this is a good idea or a dumb thing that just generates questions like this continues…