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    <p>I really like using <code>interaction</code> by agstudy - I would probably try this first. But if keeping things unchanged then:</p> <p>4 factors could be accomodated with faceting and 2 axes. Then there are 2 metrics <em>x</em> and <em>y</em>: one option is a bubble chart with both metrics distinguishing by color or shape or both (added jitter to make shapes less overlapping):</p> <pre><code>testm = melt(test, id=c('siteloc', 'modeltype', 'mth', 'yr')) # by color ggplot(testm, aes(x=siteloc, y=modeltype, size=value, colour=variable)) + geom_point(shape=21, position="jitter") + facet_grid(mth~yr) + scale_size_area(max_size=40) + scale_shape(solid=FALSE) + theme_bw() </code></pre> <p><img src="https://i.stack.imgur.com/WOhhu.png" alt="Metrics distinguished by color"></p> <pre><code>#by shape testm$shape = as.factor(with(testm, ifelse(variable=='x', 21, 25))) ggplot(testm, aes(x=siteloc, y=modeltype, size=value, shape=shape)) + geom_point(position="jitter") + facet_grid(mth~yr) + scale_size_area(max_size=40) + scale_shape(solid=FALSE) + theme_bw() </code></pre> <p><img src="https://i.stack.imgur.com/M7GpQ.png" alt="enter image description here"></p> <pre><code># by shape and color ggplot(testm, aes(x=siteloc, y=modeltype, size=value, colour=variable, shape=shape)) + geom_point(position="jitter") + facet_grid(mth~yr) + scale_size_area(max_size=40) + scale_shape(solid=FALSE) + theme_bw() </code></pre> <p><img src="https://i.stack.imgur.com/hMzg5.png" alt="enter image description here"></p> <p><strong>UPDATE:</strong></p> <p>This is attempt based on 1st comment by Dominik to show if (x,y) is above or below 1:1 line and how big is the ratio <em>x/y</em> or <em>y/x</em> - blue triangle is if x/y>1, red circle otherwise (no need in <code>melt</code> in this case):</p> <pre><code>test$shape = as.factor(with(test, ifelse(x/y&gt;1, 25, 21))) test$ratio = with(test, ifelse(x/y&gt;1, x/y, y/x)) ggplot(test, aes(x=siteloc, y=modeltype, size=ratio, colour=shape, shape=shape)) + geom_point() + facet_grid(mth~yr) + scale_size_area(max_size=40) + scale_shape(solid=FALSE) + theme_bw() </code></pre> <p><img src="https://i.stack.imgur.com/wurUz.png" alt="enter image description here"></p>
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    1. POhow to distinguish 4 factors in ggplot2?
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    1. COI think I like this better than using `interaction` but it's rather meaningless in this context. larger/smaller is not specifically of interest, but rather above or below 1:1 line. Is there an easy transformation/stat to make the circles more meaningful?
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    2. COin other words, the interest is not in (x,y) but in x/y ratio, in particular, how much it's > or < 1, correct?
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    3. COyes. I think I have something that I like, I actually removed the shape because I find different sized circles easier to compare (with red=underprediction, blue=overprediction). Is there a page that lists the shape types, I didn't see it when perusing docs.ggplot2.org/current? Also, is there anything less abstract to visually compare? I find linear distance more intuitive comparing size. Or perhaps it'd be possible to increase the number of ratio circles in the legend? Thank you for all your help
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