R help - Aug 2008 - Attempting to make a custom color spectrum to use in heatmap.2

Hello there! I'd just like to say in advance, "Thank you," for any
help
and/or advice.

My problem is as follows:

I have a dataset that is made up of percentages. I've assigned my 
"error" percentages a value of '-100', my
"non-existent" percentages a
value of '0', and all my other percentages are normal values that range 
from the high 60's to 100. I would like to create a heatmap that 
designates my "error" values as gray, my "non-existent"
values as black,
and I would like to to have the rest of my values, say 50 to 100, as a 
rainbow-type spectrum (like the palette "Spectral" in RColorBrewer, 
except with 50 values).

I've tried using breaks, and then implementing the breaks in my 
heatmap.2 command. The breaks work just fine. I guess what I want to 
control is the range of the:

col=(colorpanel(#, low="color1", mid="color2",
high="color3"))

command. Is there any way to set more values than "low,"
"mid," and
"high?" If that is possible I think it would solve my problem.
I've
looked over the documentation and searched over previous 
color/heatmap-related questions, but haven't come across anything that 
points me in the right direction.

Please let me know if any of what I said needs clarifying before you can 
give me what you feel is an appropriate response. Thanks again for your 
time.

Regards,

Daniel

colorRampPalette() may do what you want.

        -thomas


On Wed, 6 Aug 2008, Daniel Bernstein wrote:
> Hello there! I'd just like to say in advance, "Thank you,"
for any help and/or
> advice.
>
> My problem is as follows:
>
> I have a dataset that is made up of percentages. I've assigned my
"error"
> percentages a value of '-100', my "non-existent"
percentages a value of '0',
> and all my other percentages are normal values that range from the high
60's to
> 100. I would like to create a heatmap that designates my "error"
values as
> gray, my "non-existent" values as black, and I would like to to
have the rest
> of my values, say 50 to 100, as a rainbow-type spectrum (like the palette 
> "Spectral" in RColorBrewer, except with 50 values).
>
> I've tried using breaks, and then implementing the breaks in my
heatmap.2
> command. The breaks work just fine. I guess what I want to control is the
range
> of the:
>
> col=(colorpanel(#, low="color1", mid="color2",
high="color3"))
>
> command. Is there any way to set more values than "low,"
"mid," and "high?" If
> that is possible I think it would solve my problem. I've looked over
the
> documentation and searched over previous color/heatmap-related questions,
but
> haven't come across anything that points me in the right direction.
>
> Please let me know if any of what I said needs clarifying before you can
give
> me what you feel is an appropriate response. Thanks again for your time.
>
> Regards,
>
> Daniel
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
Thomas Lumley			Assoc. Professor, Biostatistics
tlumley at u.washington.edu	University of Washington, Seattle

On Wed, 2008-08-06 at 16:57 -0700, Daniel Bernstein
wrote:
> Hello there! I'd just like to say in advance, "Thank you,"
for any help
> and/or advice.
> 
> My problem is as follows:
> 
> I have a dataset that is made up of percentages. I've assigned my 
> "error" percentages a value of '-100', my
"non-existent" percentages a
> value of '0', and all my other percentages are normal values that
range
> from the high 60's to 100. I would like to create a heatmap that 
> designates my "error" values as gray, my "non-existent"
values as black,
> and I would like to to have the rest of my values, say 50 to 100, as a 
> rainbow-type spectrum (like the palette "Spectral" in
RColorBrewer,
> except with 50 values).
> 
> I've tried using breaks, and then implementing the breaks in my 
> heatmap.2 command. The breaks work just fine. I guess what I want to 
> control is the range of the:
> 
> col=(colorpanel(#, low="color1", mid="color2",
high="color3"))
> 
> command. Is there any way to set more values than "low,"
"mid," and
> "high?" If that is possible I think it would solve my problem.
I've
> looked over the documentation and searched over previous 
> color/heatmap-related questions, but haven't come across anything that 
> points me in the right direction.
> 
Hi Daniel,
You can map values to colors using "color.scale" in the plotrix
package.
What you want would require that you separate out the 50+ values to get
the graduated colors, then set the -100 and 0 values to black and gray.
Say your dataset is a matrix named "mydata", a sneaky way might be:

missval<-which(mydata == -100)
nonext<-which(mydata == 0)
# this gives you the lowest value that you want in the color range
mydata[c(missval,nonext)]<-50
# this gives you a matrix of colors that start at 50=red and
# range to 100=blue
mycellcolors<-color.scale(mydata,c(1,1,0,0),c(0,1,1,0),c(0,0,0.5,1))
# the next two lines set the colors for missing and non-existent values
mycellcolors[missval]<-"black"
mycellcolors[nonext]<-"gray"
# display the matrix as colors, using the calculated colors
color2D.matplot(mydata,cellcolors=mycellcolors)

I can't work out how to do this with "image" or
"heatmap", but someone
else might be able to tell you.

Jim