I think this can be accomplished by creating a new color column in your data frame:
data$color <- "black"
Then set the outliers to a different value:
data[outlier,"color"] <- "red"
I dont have your exact data but I think I got something similar to what you wanted using the following:
outlier <- c(1, 2, 7, 9)
data <- data.frame(x=c(1,2,3,4,5,6,7,8,9,10),
y=c(1,2,3,4,5,6,7,8,9,10))
data$color <- "black"
data[outlier,"color"] <- "red"
data
x y color
1 1 1 red
2 2 2 red
3 3 3 black
4 4 4 black
5 5 5 black
6 6 6 black
7 7 7 red
8 8 8 black
9 9 9 red
10 10 10 black
Finally plot using the new value in data:
plot(data$x, data$y, col=data$color)
Results in: