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  1. PO
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    <p>This has little to do with <strong>ggplot</strong>, but is instead a question about generating an ordering of variables to use to reorder the levels of a factor. Here is your data, implemented using the various functions to better effect:</p> <pre><code>set.seed(1234) df2 &lt;- data.frame(year = rep(2006:2007), variable = rep(c("VX","VB","VZ","VD"), each = 2), value = runif(8, 5,10), vartype = rep(c("TA","TB"), each = 4)) </code></pre> <p>Note that this way <code>variable</code> and <code>vartype</code> are factors. If they aren't factors, <code>ggplot()</code> will coerce them and then you get left with alphabetical ordering. I have said this before and will no doubt say it again; get your data into the correct format <strong>first</strong> <em>before</em> you start plotting / doing data analysis.</p> <p>You want the following ordering:</p> <pre><code>&gt; with(df2, order(vartype, variable)) [1] 3 4 1 2 7 8 5 6 </code></pre> <p>where you should note that we get the ordering by <code>vartype</code> first and only then by <code>variable</code> <em>within</em> the levels of <code>vartype</code>. If we use this to reorder the levels of <code>variable</code> we get:</p> <pre><code>&gt; with(df2, reorder(variable, order(vartype, variable))) [1] VX VX VB VB VZ VZ VD VD attr(,"scores") VB VD VX VZ 1.5 5.5 3.5 7.5 Levels: VB VX VD VZ </code></pre> <p>(ignore the <code>attr(,"scores")</code> bit and focus on the Levels). This has the right ordering, but <code>ggplot()</code> will draw them bottom to top and you wanted top to bottom. I'm not sufficiently familiar with <code>ggplot()</code> to know if this can be controlled, so we will also need to reverse the ordering using <code>decreasing = TRUE</code> in the call to <code>order()</code>.</p> <p>Putting this all together we have:</p> <pre><code>## reorder `variable` on `variable` within `vartype` df3 &lt;- transform(df2, variable = reorder(variable, order(vartype, variable, decreasing = TRUE))) </code></pre> <p>Which when used with your plotting code:</p> <pre><code>ggplot(df3, aes(x=variable, y=value, fill=vartype)) + geom_bar() + facet_grid(. ~ year) + coord_flip() </code></pre> <p>produces this:</p> <p><img src="https://i.stack.imgur.com/8lKV6.png" alt="reordered barplot"></p>
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    1. COI thank you for your solution! It works. However, i've also found, with a thorough search, that my original issue is a particular case of a common nuisance when using coord_flip().
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    2. CO@MatteoS Do you understand now why people felt this was another duplicate? The answer is the same - reorder the levels of the factor in the order you want them. The issue here was how to derive that ordering. All the **ggplot** code was superfluous and distracting. It does help to boil problems down to their base level and also tell us exactly what you want. Andrie's Answer was almost spot on until you happened to mention in comments you didn't want to enter the ordering by hand.
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    3. CONow I see, but ggplot2 is the issue here. With coord_flip(), the axis are flipped, the variables that are originally ordered L-> R are then ordered B -> T, while the legend does not match them.
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