Hi Jean,
Thanks a ton for the help. I think Im almost there, but there is still
something weird about my stuff.
I have been able to understand the color.scale() function. Now, I am trying to
plot a key for the corresponding colors. The function is called ColorBar, which
apparently works - the colors are indeed lut <- rev(heat.colors(10)) and go
from my minimum to my maximum values. However, when I try to apply this to my
mycolors( and then plot it, I suddenly have colors that seem to be outside of
the min-max (in the greens and blacks), instead of the white to red gradient.
Hope this is not too complicated of a code, but I think copy-paste it should
give the (problematic) result. I guess there is a small error somewhere, but I
cant figure out what I have done wrong :-(
Thanks a lot for any suggestion.
Patrick
#------------------------------------------------------------
library(plotrix)
#------------------------------------------------------------
# ColorBar
ColorBar <- function(lut, min, max, nticks=5, ticks=seq(min, max, len=nticks),
title='') {
scale = (length(lut)-1)/(max-min)
plot(c(min,max),c(0,10), type='n', bty='n', xaxt='n', xlab='', yaxt='n',
ylab='', main=title)
axis(1, ticks, las=1, cex.axis=0.5, lwd=0.5)
for (i in 1:(length(lut)-1)) {
y = (i-1)/scale + min
rect(y,0,y+1/scale,0.5, col=lut[i], border=NA)
}
}
#------------------------------------------------------------
# RectPlotter
RectPlotter <- function(matrixval, ycoord, height, mycolors){
rect(matrixval[,1], (ycoord-(0.4*height)), matrixval[,2],
(ycoord+(0.4*height)), col=mycolors, border = NA)
}
fake <- cbind(c(1,2,5,8,12,19), c(2,5,8,12,19,20), runif(6, 0, 2), runif(6, 0,
2), runif(6, 0, 2))
mymatrix <- fake
# Plot the color key on the lower part
lut <- rev(heat.colors(10))
minimum <- round(min(mymatrix[,-(1:2)]), digits=2)
maximum <- round(max(mymatrix[,-(1:2)]), digits=2)
ColorBar(lut=lut, min=minimum, max=maximum)
par(new=TRUE)
#____________________________________________
#_______________PROBLEM HERE_______________
mycolors <- cbind(mymatrix[,1:2],color.scale(mymatrix[,-(1:2)], extremes=lut))
plot(c(mymatrix[1,1],mymatrix[length(mymatrix[,1]),2]), c(0,1), col="White",
xlab="", ylab="", main=title, axes=F)
ycenter <- seq(from=0, to=1, length=(length(mymatrix[1,])+2))
yheight <- 1/length(ycenter)
# Plot the actual heatmap
for(i in 3:length(mymatrix[1,])){
#for(i in 3:5){
RectPlotter(mymatrix[,c(1,2,i)], ycenter[length(ycenter)-i+2], yheight,
mycolors[,i])
text(mymatrix[1,1], ycenter[length(ycenter)-i+2], colnames(mymatrix)[i],
cex=0.5, pos=4)
}
On Jan 7, 2014, at 18:48, Adams, Jean <jvad...@usgs.gov> wrote:
> Patrick,
>
> You should cc r-help on all correspondence so that others can follow the
> thread.
>
> The color range will be matched to the "x" argument you provide to the
> color.scale function (in package plotrix). So you don't need to manually
> provide the min and max yourself. If for some reason you did need to provide
> that information, you would use the xrange argument not the extremes argument
> (which is expecting colors).
>
> mycolors <- color.scale(mymatrix[,-(1:2)], c(0,1,1), c(1,1,0), c(1,0,1))
>
> Jean
>
>
> On Tue, Jan 7, 2014 at 4:16 PM, Pachapep <pacha...@gmail.com> wrote:
>
> Hi Jean
> Thanks for the quick answer. It looks like it works, but the issue is that my
> real data fluctuates between 0 and 2, so I everything is red.
> I tried using another function (color.scale), which works but gives me grey
> scale only (no colors) although I dont really understand why - its a
> detail, but it's kind of a bummer..
>
> mycolors <- color.scale(mymatrix[,-(1:2)], c(0,1,1), c(1,1,0), c(1,0,1),
> extremes=c(min(mymatrix[,-(1:2)]), max(mymatrix[,-(1:2)])))
>
> Is there a way to make an array using the min and max of the matrix (as I
> used in color.scale() above) so that the colors go from blue to red?
> Thanks again for the help.
> Patrick
>
> On Jan 7, 2014, at 15:04, Adams, Jean <jvad...@usgs.gov> wrote:
>
>> Patrick,
>>
>> You were pretty close.
>> To fix the code you have, just change "matrix" to "mymatrix" in two places,
>> and either specify the argument data= or place the heat.colors bit first in
>> the matrix function.
>>
>> Or ... you could use the array() function instead, to shorten up the code a
>> little.
>> mycol <- array(heat.colors(max(mymatrix[, 3:5]))[mymatrix[, 3:5]],
>> dim=dim(mymatrix))
>>
>> Jean
>>
>>
>> On Mon, Jan 6, 2014 at 9:19 PM, Pachapep <pacha...@gmail.com> wrote:
>> Hi all,
>> I have a matrix which I want to plot in color. I have extensively looked at
>> level plot and heatmap/heatmap.2, but I would like to be able to manage the
>> size of the bins (boxes) on my X axis. So I thought of simply using the
>> rect() function, but I cant get around assigning the correct colors to all
>> the values. I have built a RectPlotter() function that takes the start and
>> stop as well as the value assigned to each bin.
>> Here is what I have done so far (after countless hours of despair):
>>
>> RectPlotter <- function(matrixval, ycoord, height, mycolors){
>> rect(matrixval[,1], (ycoord-(0.4*height)), matrixval[,2],
>> (ycoord+(0.4*height)), col=mycolors, border = NA)
>> }
>>
>> starts <- c(1,5,8,15)
>> ends <- c(5, 8, 15, 25)
>> vals1 <- c(2, 15, 7, 13)
>> vals2 <- c(7, 2, 1, 26)
>> vals3 <- c(52, 1, 29, 18)
>> mymatrix <- cbind(starts, ends, vals1, vals2, vals3)
>> # This gives me an error
>> mycol<- matrix(nrow=dim(mymatrix)[1], ncol=dim(mymatrix)[2],
>> heat.colors(max(matrix[,3:5]))[matrix[,3:5]])
>>
>>
>> At the end, I would like to have something like a levelplot, but using the
>> starts and ends as x-axis.
>> Any help would be highly appreciated. Thanks!
>> Patrick
>> ______________________________________________
>> R-help@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.
>>
>
>
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