how to include color gradient for two variables

2018-06-10 11:07:41

My dataset for chrom 1 looks something like this

head(data)
  SNP     BP       P    Dataset          LD
1  SNP1 541095 0.00529 expression 0.000610863
2  SNP2 541095 0.07897   original 0.066610863
3  SNP3 541133 0.21990   original 0.040534557
4  SNP4 541233 0.47890 expression 0.008216450
5  SNP5 541260 0.39790   original 0.010310200
6  SNP6 541260 0.19210 expression 0.000390915
7  SNP7 541265 0.000001 original 1
7  SNP7 541265 0.00001 expression 1

I want to overlay the two datasets into one plot and also show the LD correlation of SNP7 with the other SNPs.

So far, this is what I could come up with

  Position<-data$BP/1E6
  ggplot(data, aes(x=Position, y=-log10(P), color=Dataset, shape=Dataset)) +
  geom_point(size=4) + xlim(540101/1E6,1565570/1E6) + ylim(0,10) +
  geom_hline(aes(yintercept=7), color="#a50f15")

I am not being able to group the variants according to gradient color based on LD, it shows just one color for both the datasets instead

ggplot(data, aes(x=Position, y=-log10(P), colour=LD, shape=Dataset)) +
 geom_point(size=4) + xlim(540101/1E6,1565570/1E6) + ylim(0,10) +
 geom_hline(aes(yintercept=7), color="#a50f15")

Is it possible to

1) Change the color of the dataset Original to red and expression to blue

2) make groups based on LD values

       LD values   dataset   color     dataset   color
group1 0 to 0.2    original  light blue  expression light red
group2 0.2 to 0.4  original  .         expression .
group3 0.4 to 0.6  original  .         expression .
group4 0.6 to 0.8  original  .         expression .
group5 0.8 to 1.0  original  dark blue expression dark red

Many thanks

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