facet_wrap plotting incorrect x axis co-ordinates

Question

I just don't understand this.

Here is my genomic data

structure(list(chr = c(10, 10, 11, 12, 13, 13, 17, 2, 20, 22, 
3, 3, 4, 4, 4, 4, 5, 7, 7, 8), leftPos = c(240000, 24840000, 
7200000, 6120000, 14880000, 18120000, 8760000, 53280000, 10680000, 
8640000, 13320000, 46920000, 12000000, 13560000, 16680000, 30360000, 
16440000, 2280000, 31560000, 28320000), Means.x = c(255.903115167852, 
250.944147412273, 221.51819750622, 351.093122004609, 289.007439556107, 
219.45204288982, 225.535183746474, 457.871356482534, 253.497055532121, 
252.20121505887, 342.200678275566, 373.699212483745, 1014.42590543955, 
221.696823711274, 240.80888805777, 249.180706358065, 284.401983997314, 
269.740366732235, 278.570789472848, 280.990393375634), Def.x = c(1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Means.y = c(236.86281805995, 
226.558139428814, 242.372785637286, 250.366569266078, 300.979628259253, 
241.055506095359, 227.580531582224, 373.326888100031, 212.752136489909, 
422.948449610324, 224.089190457845, 310.029877851832, 1014.42590543955, 
249.285880751277, 285.16587617125, 230.051744541219, 221.151463979895, 
289.409617875006, 317.10711734718, 262.296533161901), Def.y = c(1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1)), .Names = c("chr", 
"leftPos", "Means.x", "Def.x", "Means.y", "Def.y"), row.names = c(NA, 
-20L), class = "data.frame")

I am trying to simply plot the values of 1 according to their position (leftPos) according to each chromosome.

However using the code below:

ggplot(ZoutliersM,aes(x = ZoutliersM$leftPos,y = as.numeric(ZoutliersM$Def.x),
                         xend=ZoutliersM$leftPos,yend=0))+

  geom_point(fill="magenta",size=2,colour="red")+
  facet_wrap(~ chr)

I get the plot as follows:

This looks fine but the points are not at the correct position on the x-axis for that chromosome. For example, chromosome 22 has one point which according to the dataset should be

 chr leftPos    Means     Def
  22 8640000    422.9484   1

but when I look at the plot it is somewhere over between 20 and 30M

Why is this being plotted like this and how can I correct it? Its as if the x axis scale has nothing to do with the chart.

Answer 1

ggplot has a data argument for a reason. When you re-specify the data frame inside aes(), it overrides the subsetting and ordering done for the faceting. Just don't re-specify the name of the data frame (no mydata$column) and everything works fine:

ggplot(ZoutliersM,
       aes(x = leftPos,
           y = as.numeric(Def.x),
           xend = leftPos,
           yend = 0)) +
  geom_point(fill = "magenta", size = 2, colour = "red") +
  facet_wrap(~chr)

Now we can see that in the "22" facet, the point is a little under 10M, as expected.

Two other notes:

• specifying a "fill" for geom_point won't do anything unless you also use a shape that has separate fill and colors, such as shape = 21

• In your dput data, Def.x is already numeric, so you don't need to convert it. If it was a factor previously, make sure you convert with as.numeric(as.character(Def.x)), otherwise you'll simply be taking the levels rather than the value to numeric.