R color scatter plot points based on values

Best thing to do here is to add a column to the data object to represent the point colour. Then update sections of it by filtering.

data<- read.table('sample_data.txtt', header=TRUE, row.name=1)
# Create new column filled with default colour
data$Colour="black"
# Set new column values to appropriate colours
data$Colour[data$col_name2>=3]="red"
data$Colour[data$col_name2<=1]="blue"
# Plot all points at once, using newly generated colours
plot(data$col_name1,data$col_name2, ylim=c(0,5), col=data$Colour, ylim=c(0,10))

It should be clear how to adapt this for plots with more colours & conditions.

It's better to create a new factor variable using cut(). I've added a few options using ggplot2 also.

df <- data.frame(
  X1=seq(0, 5, by=0.001),
  X2=rnorm(df$X1, mean = 3.5, sd = 1.5)
)

# Create new variable for plotting
df$Colour <- cut(df$X2, breaks = c(-Inf, 1, 3, +Inf), 
                 labels = c("low", "medium", "high"), 
                 right = FALSE)

### Base Graphics

plot(df$X1, df$X2, 
     col = df$Colour, ylim = c(0, 10), xlab = "POS", 
     ylab = "CS", main = "Plot Title", pch = 21)

plot(df$X1,df$X2, 
     col = df$Colour, ylim = c(0, 10), xlab = "POS", 
     ylab = "CS", main = "Plot Title", pch = 19, cex = 0.5)

# Using `with()` 

with(df, 
     plot(X1, X2, xlab="POS", ylab="CS", col = Colour, pch=21, cex=1.4)
     )

# Using ggplot2
library(ggplot2)

# qplot()
qplot(df$X1, df$X2, colour = df$Colour)

# ggplot()
p <- ggplot(df, aes(X1, X2, colour = Colour)) 
p <- p + geom_point() + xlab("POS") + ylab("CS")
p

p + facet_grid(Colour~., scales = "free")

Also it'd work to just specify ifelse() twice:

plot(pos,cn, col= ifelse(cn >= 3, "red", ifelse(cn <= 1,"blue", "black")), ylim = c(0, 10))