Im using two condition wild type and treated I get  a scatter but i want to have two different colors Im not sure how to do it , I tried to group them by melting i got aesthetics error so i removed the gene column only i have two column but the data points are labelled as same  


    df <- HL_60
    #gene = df[,1]
    WT = df[,2:3]
    ATRA = df[,4:5]
    wt.mean = apply(WT,1,mean)
    atra.mean = apply(ATRA,1,mean)
    WT_ATRA = cbind.data.frame(wt.mean,atra.mean)
    head(WT_ATRA)
    
    
    
    library(ggplot2)
    library(ggpmisc)
    D1 <-WT_ATRA
    head(D1)
    my.formula  <- y ~ x
    
    p <- ggplot(data = WT_ATRA, aes(x= wt.mean,y = atra.mean) )+ geom_point(color = 'red',size = .9)+ 
      geom_smooth(method = "lm", se=FALSE, color="black", formula = my.formula) +
      stat_poly_eq(formula = my.formula,
                   eq.with.lhs = "italic(hat(y))~`=`~",
                   aes(label = paste(..eq.label.., ..rr.label.., sep = "*plain(\",\")~")), 
                   parse = TRUE) 

The figure i get is this ![one][1]

Any suggestion or help how to put two colour for two different condition would be highly appreciated 


  [1]: https://i.imgur.com/AVdWuZK.jpg
The plot is in a 2D plane which means each point has two values associated with it (x,y) in this plane. in your case, each point is a gene and has (wt_mean,atra_mean) as coordinate. So, I don't get the point of coloring on the basis of wt_mean and atra_mean. What are you trying to infer?

The plot you mentioned in the comment using fold change as a factor of color code which can be achieved with the following code in `ggplot2`.

      geom_point(aes(colour = cut(log2fc, c(-5, -1, 1, 5))),size = 2)+
      scale_color_manual(name = "Fold Change",
                         values = c("(1, 5]" = "#FF6666",
                                    "(-1,1]" = "#F5F5F5",
                                    "(-5,-1]" = "#60B9FF"),
                         labels = c("<-2", "-2< & <2", ">2"))
`log2fc` is the log2 converted foldchnage information which is divied into three different bins (-5,-1), (-1,1),(1,5). Change them according to your rquirements.