[R] making scatter plot points fill semi-transparent

[Steve Lianoglou]

Hi,

On Aug 5, 2009, at 11:48 PM, per freem wrote:

> hi all,
>
> i have a simple scatter plot, and i'd like to make it so the scatter
> plot colors are slightly transparent. i see in a previous post that
> someone mentioned the "alpha" parameter, but i am not sure how it can
> be used with the 'plot' function [*].
>
> for example, suppose i have:
>
> plot(mydata$column1, mydata$column2, col="red", cex=1)
>
> i now want to make it so the color of these points (in this case red)
> is slightly transparent, which will make overlap between them very
> obvious. i realize that hexbin and other density plot methods are used
> to make this, but i am using it for a different purpose, and so i just
> want the points to be transparent without any binning or shading.
>
> a previous poster suggested:
>
> plot( rnorm(1000), rnorm(1000), col="#0000ff22", pch=16,cex=3)
>
> but i don't understand this color notation.

It's the usual #RRGGBB color notation, w/ the last two digits  
apparently defining the amount of opacity.

#0000FFFF is blue w/ full opacity

To figure out how to define your color with RGB notation, use a mix of  
col2rgb and rgb functions:

R> col2rgb('blue', alpha=T)
       [,1]
red      0
green    0
blue   255
alpha  255

R> rgb(red=0, green=0, blue=255, alpha=255, max=255)
[1] "#0000FFFF"

Play with different values of alpha (0 < alpha <= 255) in the above  
call to get different levels of opacity for your points.

R> rgb(red=0, green=0, blue=255, alpha=10, max=255)
[1] "#0000FF0A"

R> plot( rnorm(1000), rnorm(1000), col="#0000FF0A", pch=16,cex=3)

>  is there any way to pass
> in the usual col="colorname" argument and then tweak that color's
> transparency?

Maybe, but I'm not familiar with it.

-steve

--
Steve Lianoglou
Graduate Student: Computational Systems Biology
   |  Memorial Sloan-Kettering Cancer Center
   |  Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact