Color2D.matplot uniform color range
On 12/12/2011 02:48 PM, jalfaro wrote:
Hi all.
I am having a problem using color2D.matplot
I am trying to visualize several different matrices under two color ranges.
One color range corresponds to values less than 1 and the second color range
for values greater than 1. However, the minimum value of each matrix differs
and is automatically set to have the smallest value in the color range.
Similarly, the maximum value of each matrix differs leading to non-uniform
color scales.
Below is the function that is causing me trouble. It is designed to take as
input 2 csv files with row and column headers describing a 20X20 matrix.
The goal would be to modify the code below as follows.
(1) if an entry is in range [0,1] the color scale should always be uniform
with the minimum color being 0.5 and the maximum color being 1.
(2) if an entry is in the range [1,infinity] the color scale should have
minimum color value 1 and maximum color value 3. (I used infinity simply
because there is no way of knowing how high the value will be beforehand).
Any help would be greatly appreciated.
Thanks,
Jav
library(plotrix)
make_S_figure<-function(filename,alias){
h0<- read.csv(file=filename,head=TRUE,sep=",",row.names=1)
d =data.matrix(h0)
m<- 1:20
cellcolors<-matrix(NA,nrow=20,ncol=20)
cellcolors2<--matrix(NA,nrow=20,ncol=20)
for(i in 1:length(m)){
cellcolors[d>= 1]<-color.scale(d[d>=1],cs1=c(1,1),cs2=c(1,0),cs3=c(1,0))
cellcolors[d<1]<-color.scale(d[d<1],cs1=c(0,1),cs2=c(0,1),cs3=c(1,1))
color2D.matplot(d,cellcolors=cellcolors,show.values=F,na.color="white",axes=FALSE,main=alias,
xlab="",ylab="")
axis(1,at=0.5:19.5,labels=colnames(d))
axis(2,at=0.5:19.5,labels=rev(rownames(d)))
}
Hi jalfaro, I'm not sure what you mean by a "uniform color range", so I'll provide a couple of solutions. For your values between zero and one, the code above should go from blue (0) to white (1). If the "minimum color" means that anything from 0 to 0.5 should be blue and anything from 0.5 to 1 should grade from blue to white, specify your colors like this: # you don't need a loop for this cellcolors[d<1]<-color.scale(d[d<1],cs1=c(0,0,1),cs2=c(0,0,1),cs3=1) The above will give you blue from 0 to 0.5, then scale to white at 1. What I think you want for the values of 1 and above is to scale from white to red between 1 and 3, then have red for all values above 3. So: # you don't need a loop for this either cellcolors[d >= 1 & d < 3]<- color.scale(d[d >= 1 & d < 3],cs1=1,cs2=c(1,0),cs3=c(1,0)) # no point in calling color.scale cellcolors[d >= 3]<-"red" Now, rereading your message, I think that you want to anchor the extremes of the scales regardless of the values in the matrix. If so, try this: # add the extreme values, then drop the resulting extreme colors # in the assignment to the color matrix cellcolors[d<1]<- color.scale(c(0,1,d[d<1]),cs1=c(0,0,1),cs2=c(0,0,1),cs3=1)[1:2] # same trick here, add the extremes, then drop them cellcolors[d >= 1 & d < 3]<- color.scale(c(1,3,d[d >= 1 & d < 3]), cs1=1,cs2=c(1,0),cs3=c(1,0))[-1:2] # and fill in everything greater than 3 cellcolors[d >= 3]<-"red" Let me know if you have any problems. Jim