[R] color question

[Jim Lemon]

Hi Aimin,
This example uses a log transformation to spread the colors out:

d<-read.table(text="         lateRT      earlyRT         NAD
ciLAD          LAD
 1.000000000 0.0000000000 0.006224017 0.001260241 0.0069699285
 0.000000000 1.0000000000 0.001425649 0.007418436 0.0007096344
 0.006224017 0.0014256488 1.000000000 0.064653780 0.3935566356
 0.001260241 0.0074184361 0.064653780 1.000000000 0.0024839407
 0.006969928 0.0007096344 0.393556636 0.002483941 1.0000000000",
header=TRUE)
rownames(d)<-colnames(d)
d<-as.matrix(d)
diag(d)<-NA
library(plotrix)
color2D.matplot(-log(d+0.0001),extremes=c("red","blue"),
 main="Correlation matrix of d",axes=FALSE)
axis(1,at=seq(0.5,4.5),labels=colnames(d))
axis(2,at=seq(0.5,4.5),labels=rownames(d))
color.legend(0,-0.7,2,-0.5,legend=c(0,0.001,0.007,0.07,0.4),
 rect.col=color.scale(log(c(0.00001,0.001,0.005,0.07,0.4)),
 extremes=c("blue","red")),align="rb")

Jim

On Thu, Feb 28, 2019 at 2:52 PM Aimin Yan <aimin.at.work using gmail.com> wrote:
>
> I have a question about assigning color based on the value of a matrix
>
> The following is my matrix.
>
> d
>              lateRT      earlyRT         NAD       ciLAD
> lateRT  1.000000000 0.0000000000 0.006224017 0.001260241
> earlyRT 0.000000000 1.0000000000 0.001425649 0.007418436
> NAD     0.006224017 0.0014256488 1.000000000 0.064653780
> ciLAD   0.001260241 0.0074184361 0.064653780 1.000000000
> LAD     0.006969928 0.0007096344 0.393556636 0.002483941
>                  LAD
> lateRT  0.0069699285
> earlyRT 0.0007096344
> NAD     0.3935566356
> ciLAD   0.0024839407
> LAD     1.0000000000
>
> I want to use the following function to get heatmap and dendrogram
>
> > heatmap.2(d,trace="none",margin=c(8, 10))
>
> but it is hard to use color to make  0.001260241 and 0.0074184361 to be
> visualized differently.
>
> Does anyone know how to adjust color based on these values in this matrix?
>
> Thank you,
>
> Aimin
>
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>
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