Re: [R] heatmap color specification
Jim Lemon wrote: Xiaohui wrote: ... Then, I did a heatmap for 'test' matrix. But for now, I want to specify each of the cell in the heatmap according to the values of the corresponding matrix elements of test. Let's say: col-c(red,yellow,green) for test[1,1], the color on the map should be red. I have tried par('usr') and par('mar') with rect function. But this does not work because the rect shift from the original map. Could any one tell me how to fill the cells on the map with corresponding values? Or can we get the actual coordinates of the image excluding the dendregram. Hi Xiaohui, You may be looking for something like color2D.matplot in the plotrix package or image in the graphics package. Jim Thanks, Jim. I found this problem can be solve with the 'scale' parameter specified to FALSE. If it is TRUE, then the positive integer is scale to a real number which will cause the problem earlier. Xiaohui __ R-help@stat.math.ethz.ch 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.
Re: [R] heatmap color specification
Xiaohui wrote: ... Then, I did a heatmap for 'test' matrix. But for now, I want to specify each of the cell in the heatmap according to the values of the corresponding matrix elements of test. Let's say: col-c(red,yellow,green) for test[1,1], the color on the map should be red. I have tried par('usr') and par('mar') with rect function. But this does not work because the rect shift from the original map. Could any one tell me how to fill the cells on the map with corresponding values? Or can we get the actual coordinates of the image excluding the dendregram. Hi Xiaohui, You may be looking for something like color2D.matplot in the plotrix package or image in the graphics package. Jim __ R-help@stat.math.ethz.ch 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.
[R] heatmap color specification
hi, I have a positive integer matrix like: test-matrix(c(1,2,2,2,2,1,1,2,3),3) and based on the distant function I made like this: generateDistMat-function (target) { n - nrow(target) rn - rownames(target) distM - matrix(NA, n, n) diag(distM) - 0 for (i in 1:(n - 1)) for (j in (i + 1):n) { distM[i, j] - length(which(target[i, ] != target[j, ])) distM[j, i] - distM[i, j] } colnames(distM) - rownames(distM) - rn distM } dist.fun - function(M) return(as.dist(generateDistMat(M))) Then, I did a heatmap for 'test' matrix. But for now, I want to specify each of the cell in the heatmap according to the values of the corresponding matrix elements of test. Let's say: col-c(red,yellow,green) for test[1,1], the color on the map should be red. I have tried par('usr') and par('mar') with rect function. But this does not work because the rect shift from the original map. Could any one tell me how to fill the cells on the map with corresponding values? Or can we get the actual coordinates of the image excluding the dendregram. Any help would be appreciated. Thanks in advance! Xiaohui __ R-help@stat.math.ethz.ch 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.
[R] Heatmap color specification
hi, I have a positive integer matrix like: test-matrix(c(1,2,2,2,2,1,1,2,3),3) and based on the distant function I made like this: generateDistMat-function (target) { n - nrow(target) rn - rownames(target) distM - matrix(NA, n, n) diag(distM) - 0 for (i in 1:(n - 1)) for (j in (i + 1):n) { distM[i, j] - length(which(target[i, ] != target[j, ])) distM[j, i] - distM[i, j] } colnames(distM) - rownames(distM) - rn distM } dist.fun - function(M) return(as.dist(generateDistMat(M))) Then, I did a heatmap for 'test' matrix. But for now, I want to specify each of the cell in the heatmap according to the values of the corresponding matrix elements of test. Let's say: col-c(red,yellow,green) for test[1,1], the color on the map should be red. I have tried par('usr') and par('mar') with rect function. But this does not work because the rect shift from the original map. Could any one tell me how to fill the cells on the map with corresponding values? Or can we get the actual coordinates of the image excluding the dendregram. Any help would be appreciated. Thanks in advance! Xiaohui __ R-help@stat.math.ethz.ch 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.