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When I make a histogram I get the actual distribution of my samples, with the appropriate counts, but when I try making a density plot the scales go up to 800, and when I try using geom_density(aes(y = after_stat(count)) I get a y-axis scaled in the 1000s. I assume this is the expected behaviour of ggplot2, but I just don't understand the theory behind this.

Here are the histograms:

enter image description here

Here are the normal density plots:

enter image description here

And here's the density plots with after_stat(count):

enter image description here

Edit:

The x axis represents percentages I calculated manually to aggregate the lipid concentrations I was given. So it's something like "percentage of total lipid concentration", that's why the x axes don't always start at 0. Was I wrong to represent percentages in histograms/density plots?

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    $\begingroup$ Your last set of plots looks like it's mis-labeled: "count" should read "density." $\endgroup$
    – whuber
    Feb 26 at 15:10
  • $\begingroup$ @whuber I'm not sure how to label it when I'm trying to scale it by count. Should it just read density? $\endgroup$ Feb 26 at 16:10
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    $\begingroup$ Upon closer inspection, I would be cautious about that, because the third panel of plots clearly does not show densities, either: the areas of the curves tend to be much larger than $1.$ They appear to be densities multiplied by total counts. $\endgroup$
    – whuber
    Feb 26 at 16:31
  • $\begingroup$ Suggested title change. Do edit it back if it's not accurate. $\endgroup$
    – Nick Cox
    Feb 27 at 8:02
  • $\begingroup$ It would help to know what the units of the X axis are, if only because it would make the graphs easier to talk about. But supposing that Y is "count" and X is "seconds", in the original plots; then the density plots would have a Y axis unit of "counts per second". This should make the scaling of the density plots intuitive. (The stuff with after_stat I have no idea, so if that was your actual question, sorry for being redundant.) $\endgroup$ Feb 27 at 18:12

2 Answers 2

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The bottom line (here at the top) is that the vertical scale in the second series of plots is probability density, which not only is not the count or frequency in any bin, it is not probability either. It is the probability per unit, where the unit (of measurement) is the unit of whatever is plotted on the horizontal axis.

The rule is that the probability density (probability per unit) adds (strictly, integrates) to 1 over the total support. To see this, think of a uniform (rectangular, flat) distribution on [0, 1]. The range is 1, the probability density is constant at 1, and

total probability = average density over the range $\times$ the range

OR

1 = 1 (this average is easy, as density is constant) $\times$ 1.

Now halve the variable so that the distribution is on [0, 0.5]. The total probability remains the same and so the average density must double to 2. Or double it, and the converse is observed.

Checking out your second series of plots underlines that as the horizontal range increases numerically, even though the specific units may well vary from plot to plot, so also the typical densities decrease. This inverse relationship arises from the fact that total probability is constant at 1.

The top left distribution has a range of about 0.007, so the average density must be about 1/ 0.007 or about 140, which does not quite match the numbers on the probability density axis. At the same time, it seems that the plots are all truncated, so the set-up is presumably complicated by that at least.

In principle, this is nothing whatever to do with your use of R or ggplot2. It is standard statistically.

Important detail: What the third series of plots shows is not so clear to me. Perhaps it is frequency density.

One way to check what any routine does is to feed it a very simple dataset for which you can work out in advance what the results should be. E.g. 100 values of integers 0 to 9 with equal frequencies of 10.

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  • $\begingroup$ yeah, I know it's not because of R, but I couldn't understand the statistics behind it and I didn't know how to ask the question without just showing what I asked ggplot to do. $\endgroup$ Feb 26 at 16:09
  • $\begingroup$ But the first plot truncated, so why wouldn't the numbers match? $\endgroup$ Feb 26 at 16:15
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    $\begingroup$ The code you used is relevant to the exact results shown, as is the full range of each variable. I can't usefully speculate beyond that as you don't give access to your data, you don't show your exact code, and I don't want to look inside R or at R documentation to work out what is going on. But a one-sentence summary that Your results appear to show probability density and so the numbers shown depend on units of measurement seems to encapsulate the story here. $\endgroup$
    – Nick Cox
    Feb 26 at 16:21
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The difference between the two figures is that one displays the probability density and the other the count density.

The total probability is always one (by definition). But the total counts can be different for the three groups. This makes that the relative scales of the two different density plots is different.

For example: in the c19 steroids measurements you have only 3 cases from the control group and 13 cases from the hyper group. (I am guessing those numbers based on your histogram below)

counting numbers

So the number/count density for the hyper group is much higher than the number/count density for the control group. (see below the green curves/area which is much higher than the red curve/area)

counts density compared

When you use probability density, then the scale for each distribution is seperately normalized, such that the total area under the curve equals to 1. (It is the integral that needs to sum up to 1, below this is roughly estimated with two rectangles that seem to have a similar area as the area under the curves)

comparing probability density

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