Beeswarm plot in R: weird gaps?

Question

I've made a beeswarm plot in R by basically looping through groups in my data and creating a beeswarm for each group and combining into one plot:

#Build color field
color.By.Category <- function(x) {
  if (x == "Polydrug") {
    return("red")
  } else if (x == "Opioid") {
    return("blue")
  } else if (x == "Cocaine") {
    return("green")
  } else if (x == "Gabapentin") {
    return("orange")
  } else if (x == "Meth") {
    return("blue")
  } else if (x == "Benzo") {
      return("pink")
  } else {
    return("black")
  }
}



# Make 5 rows, the first is the legend
par(mfrow=c(5,1), mar=c(0,10,0,0), oma=c(10,0,5,2), bg="black")


# Build legend
drug.categories <- unique(death.data.2$drug)
colr <- sapply(drug.categories, color.By.Category)
xleg <- seq(-10,110, by=23)
beeswarm(xleg, pwcol=colr, 
         horizontal = TRUE, 
         pch=15, 
         method="center", 
         cex=1, 
         xlim=c(-10,110), 
         ylim=c(-10,4))
text(x=xleg+0, y=.5, labels=toupper(drug.categories), col="white", pos=4, cex=1.1)

races <- unique(death.data.2$race)


for (i in 1:length(races)) {

  # Subset to race/ethnicity
  current <- death.data.2[death.data.2$race == races[i],]

  # Draw the symbols
  beeswarm(current$age, pwcol=current$color,
           pch=15, method="center",
           cex=1, horizontal=TRUE,
           ylim=c(-10,10), xlim=c(0,100), axes=FALSE)

  #  label
  mtext(races[i], side = 2, las=1, col="white", cex=.9)
}

x <- seq(0, 100, 5)
axis(side = 1, labels = x, at=x, col="black", col.ticks = "white")
mtext(x, side = 1, outer=FALSE, at=x, line=.8, col="white", cex=.8)
mtext("Age", side=1, at=x[1], outer=FALSE, col="white", line=2, adj=0.05, padj=.5, cex=.8)


# Title
mtext("Overdose Deaths by Substance Type", side=3, outer=TRUE, line=1, cex=1.5, col="white")

Which looks like this:

You can see there are weird gaps (i.e. blank lanes) where no data is showing, which almost looks like some kind of artifact from how the plot is rendering. What's going on here?

Without sample data, it's easy to surmise either (or both): (1) your data has gaps for some reason; while unexpected, it may also indicate an issue with the data retrieval, recording, and/or processing; or (2) plotting artifacts due to dpi issues in a raster canvas, where a vector (pdf, svg) format might allow you to zoom in and remove the artifact; this is more common (in experience) with lines not tiles/beeswarm, so I don't think this is it (atm). If you can share the data somehow, others can look at this, otherwise it's too plausibly #1 in my book. — r2evans, Jul 12 '22 at 11:46
The `rate` of drop appears consistently 5, is Gabapentin actually ever printed? Nice hypodermic results given context. — Chris, Jul 12 '22 at 12:35

score 0 · Accepted Answer · answered Jul 13 '22 at 13:08

I believe you can remove the gaps by setting breaks = NA in your "Draw the symbols" beeswarm() call. The help file ?beeswarm tells us

breaks Breakpoints (optional). If NULL, breakpoints are chosen automatically. If NA, bins are not used (similar to stripchart with method = "stack").

So when the breaks = NA the binning behavior is prevented and the gaps should not appear.

# Draw the symbols
  beeswarm(current$age, pwcol=current$color,
           pch=15, method="center",
           cex=1, horizontal=TRUE,
           ylim=c(-10,10), xlim=c(0,100), axes=FALSE, breaks = NA)

Beeswarm plot in R: weird gaps?

1 Answers1