In the third and last of the ggplot series, this post will go over interesting ways to visualize the distribution of your data. I will make up some data, and make sure to set the seed.
library(ggplot2) library(gridExtra) set.seed(10005) xvar <- c(rnorm(1500, mean = -1), rnorm(1500, mean = 1.5)) yvar <- c(rnorm(1500, mean = 1), rnorm(1500, mean = 1.5)) zvar <- as.factor(c(rep(1, 1500), rep(2, 1500))) xy <- data.frame(xvar, yvar, zvar)
>> HistogramsI've already done a post on histograms using base R, so I won't spend too much time on them. Here are the basics of doing them in ggplot. More on all options for histograms here. The R cookbook has a nice page about it too: http://www.cookbook-r.com/Graphs/Plotting_distributions_(ggplot2)/ Also, I found this really great aggregation of all of the possible geom layers and options you can add to a plot. In general the site is a great reference for all things ggplot.
#counts on y-axis g1<-ggplot(xy, aes(xvar)) + geom_histogram() #horribly ugly default g2<-ggplot(xy, aes(xvar)) + geom_histogram(binwidth=1) #change binwidth g3<-ggplot(xy, aes(xvar)) + geom_histogram(fill=NA, color="black") + theme_bw() #nicer looking #density on y-axis g4<-ggplot(xy, aes(x=xvar)) + geom_histogram(aes(y = ..density..), color="black", fill=NA) + theme_bw() grid.arrange(g1, g2, g3, g4, nrow=1) ## stat_bin: binwidth defaulted to range/30. Use 'binwidth = x' to adjust ## this. stat_bin: binwidth defaulted to range/30. Use 'binwidth = x' to ## adjust this. stat_bin: binwidth defaulted to range/30. Use 'binwidth = x' ## to adjust this.Notice the warnings about the default binwidth that always is reported unless you specify it yourself. I will remove the warnings from all plots that follow to conserve space.
>> Density plotsWe can do basic density plots as well. Note that the default for the smoothing kernel is gaussian, and you can change it to a number of different options, including kernel=“epanechnikov” and kernel=“rectangular” or whatever you want. You can find all of those options here.
#basic density p1<-ggplot(xy, aes(xvar)) + geom_density() #histogram with density line overlaid p2<-ggplot(xy, aes(x=xvar)) + geom_histogram(aes(y = ..density..), color="black", fill=NA) + geom_density(color="blue") #split and color by third variable, alpha fades the color a bit p3<-ggplot(xy, aes(xvar, fill = zvar)) + geom_density(alpha = 0.2) grid.arrange(p1, p2, p3, nrow=1)
>> Boxplots and moreWe can also look at other ways to visualize our distributions. Boxplots are probably the most useful in order to describe the statistics of a distribution, but sometimes other visualizations are nice. I show a jitter plot and a volcano plot. More on boxplots here. Note that I removed the legend from each one because it is redundant.
#boxplot b1<-ggplot(xy, aes(zvar, xvar)) + geom_boxplot(aes(fill = zvar)) + theme(legend.position = "none") #jitter plot b2<-ggplot(xy, aes(zvar, xvar)) + geom_jitter(alpha=I(1/4), aes(color=zvar)) + theme(legend.position = "none") #volcano plot b3<-ggplot(xy, aes(x = xvar)) + stat_density(aes(ymax = ..density.., ymin = -..density.., fill = zvar, color = zvar), geom = "ribbon", position = "identity") + facet_grid(. ~ zvar) + coord_flip() + theme(legend.position = "none") grid.arrange(b1, b2, b3, nrow=1)
>> Putting multiple plots togetherFinally, it's nice to put different plots together to get a real sense of the data. We can make a scatterplot of the data, and add marginal density plots to each side. Most of the code below I adapted from this StackOverflow page. One way to do this is to add distribution information to a scatterplot as a “rug plot”. It adds a little tick mark for every point in your data projected onto the axis.
#rug plot ggplot(xy,aes(xvar,yvar)) + geom_point() + geom_rug(col="darkred",alpha=.1)