Re: [R] microarray-like graph

From: Eric Hu <list.eric_at_gmail.com>
Date: Sat 20 May 2006 - 06:43:56 EST

Thanks Jim. This is almost what I want. One problem is that the colors are not mixing at the same position and the latter color simply overwrites the previous one if their V4 and V6 are similar. I am wondering if 1) somehow the colors can be mixed at the same position or 2) bin V6 at some interval to get an average single value for that range. What do you think? Thanks.

Eric

On 5/19/06, Jim Lemon <jim@bitwrit.com.au> wrote:
>
> Eric Hu wrote:
> > Hi, I am beginning to learn R and have a data table that I would like to
> > produce a microarray-like plot. The table looks like this:
> >
> > 3 0 0 3 -377.61 1.94
> > 3 0 0 3 -444.80 2.36
> > 2 1 0 3 -519.60 2.39
> > 1 1 1 3 -54.88 2.49
> > 2 1 1 4 -536.55 2.53
> > 1 0 1 2 108.29 2.62
> > 2 0 0 2 39.56 2.62
> > 3 0 1 4 108.32 2.63
> > 2 0 0 2 -455.23 2.84
> > 1 0 0 1 -432.30 2.98
> > ...
> >
> > I would like to assign colors to the first three columns and plot the
> last
> > column against fourth column which is the sum of the first three at each
> > row. Can anyone point to me how to approach this? Thanks for your
> > suggestions.
> >
> Hi Eric,
>
> Here is an initial try at your plot. I doesn't look great, but you may
> be able to use some of the ideas.
>
> hu.df<-read.table("hu.dat")
> > hu.df
> V1 V2 V3 V4 V5 V6
> 1 3 0 0 3 -377.61 1.94
> 2 3 0 0 3 -444.80 2.36
> 3 2 1 0 3 -519.60 2.39
> 4 1 1 1 3 -54.88 2.49
> 5 2 1 1 4 -536.55 2.53
> 6 1 0 1 2 108.29 2.62
> 7 2 0 0 2 39.56 2.62
> 8 3 0 1 4 108.32 2.63
> 9 2 0 0 2 -455.23 2.84
> 10 1 0 0 1 -432.30 2.98
> hu.col<-rgb(hu.df$V1,hu.df$V2,hu.df$V3,maxColorValue=3)
> hu.col
> [1] "#BF0000" "#BF0000" "#804000" "#404040" "#804040" "#400040"
> "#800000"
> [8] "#BF0040" "#800000" "#400000"
> plot(hu.df$V6,hu.df$V4,col=hu.col,pch=15,cex=3)
>
> Jim
>

        [[alternative HTML version deleted]]



R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Sat May 20 06:51:19 2006

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.1.8, at Sat 20 May 2006 - 08:10:16 EST.

Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-help. Please read the posting guide before posting to the list.