[R] Levelplots with non-continuous x-axis breaks
Pachapep
pachapep at gmail.com
Wed Jan 8 22:59:20 CET 2014
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 doesn’t correspond to that in the key (it is red-ish in the plot while the 1 corresponds to yellow-ish in the key), so I’m 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 <jvadams at 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 <pachapep at gmail.com> wrote:
>
> Hi Jean,
> Thanks a ton for the help. I think I’m 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 can’t 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 <jvadams at 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 <pachapep at 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 don’t really understand why - it’s 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 <jvadams at 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 <pachapep at 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 can’t 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 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.
>>>
>>
>>
>
>
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