Q:

Plot points below a certain value

I would like to plot only the points which d1 is less than 0.2 for them. 
library(ggplot2)

ggplot(data, aes(x=data$d1, y=data$d2)) + 
  geom_point(aes(colour = mydata))

A:

ggplot plots the data you give it.  If you only want it to plot a subset of your data, only give it a subset of your data:
ggplot(subset(data, d1 < 0.2), aes(x = d1, y = d2)) + 
  geom_point(aes(colour = mydata))

Also, don't use data$column inside aes()--just use unquoted column names. 

A:

You can filter the points in your data feeding into ggplot function.  Please notice that you don't need data$ in aes; you can simply use the variable name.  Here, I am using iris dataset since you haven't provided your data. 
library(ggplot2)

ggplot(iris[iris$Sepal. Length<5,], aes(x=Sepal. Length, y=Sepal. Width)) + 
  geom_point(aes(colour = Species))

In your case, it'd be:
ggplot(data[data$d1<0.2,], aes(x=d1, y=d2)) + 
  geom_point(aes(colour = mydata))

