Patrick,
No error in your code, just two different ways of deriving a range of
colors ... heat.colors() and color.scale(). I modified the code to just
use color.scale(). You can tell it what two colors you want it to use for
the extremes, and it will work out the shades in between.
Jean
# fake data
fake <- cbind(c(1,2,5,8,12,19), c(2,5,8,12,19,20), c(1,1,1,1,1,1),
runif(6, 0, 2), runif(6, 0, 2))
mymatrix <- fake
dimnames(mymatrix)[[2]] <- letters[1:dim(fake)[2]]
# separate the first two columns from the remaining columns for simplicity
mymatrix12 <- mymatrix[, 1:2]
mymatrix3plus <- mymatrix[, -(1:2)]
# create variables for the dimensions for easy reference later
nrows <- dim(mymatrix3plus)[1]
ncols <- dim(mymatrix3plus)[2]
# to make sure that the min and max contain all of the data
# use floor(100*...)/100 and ceiling(100*...)/100 instead of round(..., 2)
datalim <- c(floor(100*min(mymatrix3plus)),
ceiling(100*max(mymatrix3plus)))/100
# choose two colors to be the end points
colorlim <- c("yellow", "red")
# create a sequence of 10 colors across the selected range for the legend
lut <- color.scale(seq(datalim[1], datalim[2], length=10),
extremes=colorlim, xrange=datalim)
# it's not clear from the help file, but the extremes= argument wants a
range (a vector of length 2)
mycolors <- array(color.scale(mymatrix3plus, extremes=colorlim,
xrange=datalim), dim=dim(mymatrix3plus))
ycenter <- seq(from=0, to=1, length=(nrows + 2))
yheight <- 1/(nrows + 2)
# Plot the color key on the lower part
ColorBar(lut=lut, min=datalim[1], max=datalim[2])
# Plot the actual heatmap
par(new=TRUE)
# can't use title for main= argument, because title only exists inside the
ColorBar() function
plot(c(mymatrix12[1, 1], mymatrix12[nrows, 2]), c(0, 1), col="White",
xlab="", ylab="", main="SOMETHING", axes=F)
for(i in 1:ncols){
RectPlotter(mymatrix12, ycenter[nrows - i + 2], yheight, mycolors[, i])
text(mymatrix12[1,1], ycenter[nrows - i + 2], colnames(mymatrix3plus)[i],
pos=4)
}
On Wed, Jan 8, 2014 at 3:59 PM, Pachapep <pacha...@gmail.com> wrote:
>
> Hi Jean,
> Thanks for the great help. Indeed, it seems that that helps a bit.
> However, I included a control column made of ones.
>
> fake <- cbind(c(1,2,5,8,12,19), c(2,5,8,12,19,20), c(1,1,1,1,1,1),
> runif(6, 0, 2), runif(6, 0, 2), runif(6, 0, 2))
>
>
> However, the color doesnt correspond to that in the key (it is red-ish in
> the plot while the 1 corresponds to yellow-ish in the key), so Im not sure
> whether it is the key or the colors that are messed up. Sorry for all these
> questions.. and thanks (again) for the help provided.
>
>
>
>
>
>
>
> On Jan 8, 2014, at 16:15, Adams, Jean <jvad...@usgs.gov> wrote:
>
> Patrick,
>
> Thanks for providing reproducible code!
>
> I think the main problem was that the extremes= argument in the
> color.scale() function wants a range (a vector of length 2), and you were
> providing with more than that, length(lut) is 10.
>
> In the process of tracking this down, I made a bunch of minor changes to
> your code to help me see what was going on. This is what I ended up with.
>
> Jean
>
>
>
> # fake data
> fake <- cbind(c(1,2,5,8,12,19), c(2,5,8,12,19,20), c(1,1,1,1,1,1),
> runif(6, 0, 2), runif(6, 0, 2), runif(6, 0, 2))
>
> mymatrix <- fake
> dimnames(mymatrix)[[2]] <- letters[1:5]
>
> # separate the first two columns from the remaining columns for simplicity
> mymatrix12 <- mymatrix[, 1:2]
> mymatrix3plus <- mymatrix[, -(1:2)]
> # create variables for the dimensions for easy reference later
> nrows <- dim(mymatrix3plus)[1]
> ncols <- dim(mymatrix3plus)[2]
>
> # prepare plotting parameters
> lut <- rev(heat.colors(10))
> # to make sure that the min and max contain all of the data
> # use floor(100*...)/100 and ceiling(100*...)/100 instead of round(..., 2)
> minimum <- floor(100*min(mymatrix3plus))/100
> maximum <- ceiling(100*max(mymatrix3plus))/100
> # it's not clear from the help file, but the extremes= argument wants a
> range (a vector of length 2)
> mycolors <- color.scale(mymatrix3plus, extremes=lut[c(1, length(lut))])
> ycenter <- seq(from=0, to=1, length=(nrows + 2))
> yheight <- 1/(nrows + 2)
>
> # Plot the color key on the lower part
> ColorBar(lut=lut, min=minimum, max=maximum)
>
> # Plot the actual heatmap
> par(new=TRUE)
> # can't use title for main= argument, because title only exists inside the
> ColorBar() function
> plot(c(mymatrix12[1, 1], mymatrix12[nrows, 2]), c(0, 1), col="White",
> xlab="", ylab="", main="SOMETHING", axes=F)
> for(i in 1:ncols){
> RectPlotter(mymatrix12, ycenter[nrows - i + 2], yheight, mycolors[, i])
> text(mymatrix12[1,1], ycenter[nrows - i + 2],
> colnames(mymatrix3plus)[i], pos=4)
> }
>
>
>
> On Wed, Jan 8, 2014 at 2:13 PM, Pachapep <pacha...@gmail.com> wrote:
>
>>
>> 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<http://www.r-project.org/posting-guide.html>
>>>> and provide commented, minimal, self-contained, reproducible code.
>>>>
>>>
>>>
>>>
>>
>>
>
>
>
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