ok, I think I got it. Here is the code I used. Thanks for the help guys..
fake <- cbind(c(1,2,5,8,12,19), c(2,5,8,12,19,20), c(1,1,1,1,1,1),
c(-10,-10,-10,-10,-10,-10), c(10,10,10,10,10,10), runif(6, 0, 2), runif(6, 0,
2))
datalim <- c(-0,10)
matrix3plus <- fake[,-(1:2)]
dimnames(fake)[[2]] <- letters[1:dim(fake)[2]]
rbPal <- colorRampPalette(c('blue', 'white','red'))
gradcol <- rbPal(100)
mycolors <- cbind(fake[,1:2], array(rbPal(100)[as.numeric(cut(matrix3plus,
breaks=100))], dim=dim(matrix3plus)))
# Plot the color key on the lower part
ColorBar(lut=gradcol, min=datalim[1], max=datalim[2])
par(new=TRUE)
plot(c(fake[1,1],fake[length(fake[,1]),2]), c(0,1), col="White", xlab="",
ylab="", main=title, axes=F)
yheight <- 1/length(ycenter)
ycenter <- seq(from=0, to=1, length=(length[fake[1,]]))
trackheight <- ycenter[2]
for(i in 3:length(fake[1,])){
RectPlotter(matrixval=fake[,c(1,2,i)],
ycoord=ycenter[length(ycenter)-i+2-emptylines], trackheight=ycenter[2],
mycolors=mycolors[,i])
text(fake[1,1], ycenter[length(ycenter)-i+2-emptylines], colnames(fake)[i],
cex=cexsize, pos=4)
}
On Jan 10, 2014, at 15:47, Pachapep <[email protected]> wrote:
> Sorry for bugging you again. I was wondering whether it is possible to
> include multiple different colors instead of just two.
> In the example below, the color.scale() function goes from yellow to red, but
> never passes through plain white. Would it be possible to tweak the function
> or would I have to start all over again?
> Thanks for any tips.
> patrick
>
> On Jan 9, 2014, at 7:54, Pachapep <[email protected]> wrote:
>
>>
>> Great, it works perfectly! Thanks so much for the awesome help!
>> (Happy) patrick
>>
>> On Jan 9, 2014, at 7:07, Adams, Jean <[email protected]> wrote:
>>
>>> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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
>>>>>> ______________________________________________
>>>>>> [email protected] 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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