I'm trying to plot a scatter plot with points coloured by their log2 value in the following data: 

```
   chromosome start   end test  ref position        log2      p.value cnv cnv.size cnv.log2 cnv.p.value
1           X     1 10000   50   74     5000 -0.29260198 2.857792e-06   0       NA       NA          NA
2           X  5001 15000   50   72    10000 -0.25307362 4.125984e-05   0       NA       NA          NA
10          X 45001 55000  992 1043    50000  0.20066806 7.482412e-04   0       NA       NA          NA
11          X 50001 60000 1287 1417    55000  0.13416749 1.687005e-02   0       NA       NA          NA
12          X 55001 65000  892 1149    60000 -0.09226799 7.342756e-02   0       NA       NA          NA
13          X 60001 70000  651  838    65000 -0.09129751 7.556642e-02   0       NA       NA          NA

```

I'm trying to colour by log2 values where: 

* higer positive values are dark blue and solid
* lower positive values are light blue and more transparent
* values in range -0.75:0.75 are white
* lower negative values are light red and more transparent
* higher negative values are dark red and solid

I've tried to achieve this by plotting the pos and neg values separately: 

```
pos<-subset(clean_file, clean_file$log2 > 0)
neg<-subset(clean_file, clean_file$log2 < 0)

p <- ggplot()
p <- p + geom_point(data=pos, aes(x = start, y = log2, alpha = log2, colour = log2))
p <- p + scale_colour_gradient2(low=muted("blue"), high=muted("green"), limits=c(0, 0.75), na.value="black" )   
p <- p + geom_point(data=neg, aes(x = start, y = log2, alpha = -log2, colour = -log2))
p <- p + scale_colour_gradient2(low=muted("purple"), high=muted("red"), limits=c(0, -0.75), na.value="darkred" )
p <- p + ylim(-5,5)
p <- p + facet_wrap(~chromosome, scale="free_x")

```

But the result is not right (and I get the following error):

> 
> Scale for 'colour' is already present. Adding another scale for
>  'colour', which will replace the existing scale.
> 
> 
> 

[![enter image description here](https://i.stack.imgur.com/1fqXc.png)](https://i.stack.imgur.com/1fqXc.png)