Plotting Contrasting graph(s) from a dataset using R

Question

Dear R users,

I have a set of data (1000+ animals) from two seasons (winter and summer) and would like to demonstrate the differences in the gestation length (days) pattern in these two seasons. My data is similar to this:

id <- c(1,2,3,4,5,6,7,8,9,10)
season <- c(1,1,2,2,1,2,1,1,2,1)
gest <- c(114,NA,123,116,NA,120,110,NA,116,119)

data <- cbind(id,season,gest)

I would like to have something like this:

http://had.co.nz/ggplot2/graphics/55078149a733dd1a0b42a57faf847036.png

OR any similar form of graph that would give me a good contrast.

Thank you for all your help,

Bazon

Answer 1

There is a chart type commonly used to show demographics data, and in particular for directly contrasting two groups in which you wish to emphasize the comparison of subgroups that comprise both groups which are identical to each other along some or all variables other than In the demographics context, the most common application is age structure of males versus females. This seems like it might be a good candidate to effectively visualize your data.

The plot shown below was created using the Base graphics package in R and the (excellent) R Package SVGAnnotation, by Duncan Temple Lang, to create the interactive elements (by re-rendering the image in SVG and post-processing the resultant XML).

(Although the plot was created using R and SVGAnnotate, the image below is from a UK Government Site).

Answer 2

That particular plot that you linked used ggplot2. I'm not really good at using it, so I'll show you how to do it with base graphics

data <- as.data.frame(data)
d1 <- density(data$gest[which(data$season==1)], na.rm=TRUE)
d2 <- density(data$gest[which(data$season==2)], na.rm=TRUE)
plot(d1, ylim=c(0, max(d1$y,d2$y)), xlim=range(c(d1$x, d2$x)),
  main="Length of gestation", xlab="Length (days)", col="blue", lwd=2)
polygon(d1$x, d1$y, col=rgb(0, 0, 1, 0.5), lty=0)
points(d2, t="l", col="red", lwd=2)
polygon(d2$x, d2$y, col=rgb(1, 0, 0, 0.5), lty=0)

Alternatively check out the densityplot function of the lattice package, although I'm not sure how to fill in the lines.

PS: is your dataset that small? Density plots are probably NOT the way to go if that is the case (a scatterplot would be better)

EDIT

If you want to do this with histograms you can do something like:

hist(data$gest[which(data$season==1)], main="Length of gestation", 
    xlab="Length (days)", col=rgb(0, 0, 1, 0.5))
# Note the add=TRUE parameter to superimpose the histograms
hist(data$gest[which(data$season==2)], col=rgb(1, 0, 0, 0.5), add=TRUE)

Answer 3

library(ggplot2)
df <- data.frame(id=id,season=season,gest=gest)
qplot(gest,data=df,geom="density",fill=season,alpha=I(0.2))

This should give something similar to that example, but you may want to play with the alpha parameter to get the transparency right.