similar to: heatmap.2 with colsep and sepwidth

I have written a wrapper for heatmap.2 called heatmap.w.row.and.col.clust which auto-generates breaks using breaks<-round((c(seq(from=(-20 * stddev), to=(20 * stddev))))/20, digits = 2) #(stddev in this case = 2.5) This has always worked well in the past but now I am getting an error that non-finite breaks are being generated. Drilling down, it seems that my wrapper is generating finite

I'm using this code to create a heatmap of expression data and indicate a specific column of data, post clustering: #Generate heatmap: heatmapChipDx <- heatmap.2(L3data_med2, dendrogram="column",trace="none", col=redgreen(64), colsep=seps, sepcolor="yellow", sepwidth = 0.1, margin=c(5,5), scale="row", key=FALSE) I have two problems that I'm

Hello, I'm trying to learn how to use lattice and levelplot in particular. There are three elements of customizing the plots I'm stuck with: a) Is there a way to put borders around each "cell" within a level-plot. I'm trying to do something like the colsep/rowsep/sepcolor/sepwidth parameters of heatmap.2 in gplots b) Can I alter the line-width of dendrogram added

Hello again, lately I have been playing a lot with heatmap functions, in particular I complemented heatmap.2 with a nice feature from heatmap.plus, i.e. the possibility of assigning a matrix to ColSideColors so to take into account more annotations. Below is the code I introduced in heatmap.2, everything else is maintained equal to heatmap.2: if (!missing(ColSideColors)) { #if

Dear List, I want to use transparency in R to represent downweighting of observations based on clusters (repeated observations in a dataset). Some clusters will have identical covariate values in a parameter space -- in the 2D x,y case, these represent a bunch of semi-tranparent dots in the same place. I'd like these overlapping dots to be completely opaque. In other cases, the

Hello, I can't seem to add transparency to any color ramp I create using colorRampPalette(). Can someone tell me if it is possible to create transparent colour ramps? I am attempting to map shaded relief under elevation data. I know I can use the terrain.colors() with the alpha option, but I would prefer to create my own colour ramp using more vibrant colours. My most recent attempt at

Dear R users, I'm trying to create images of 2 symmetrical matrices using heatmap.2 of the 'gplots' library. Both matrices have the same row and column names For the first matrix I'm using the default clustering and column denrogram options: heatmap.2(Matrix1, symm=T, breaks=20, col=rich.colors(19), main="matrix1", density.info="histogram",

Hi Allen and list, See the code below.? I've tried it on R2.13 and R2.8.0 using either heatmap.plus 1.3 or the latest.? All gave the same results.? The problem is in the last line: when I tried to plot two different color bars, the one corresponding to "cm.colors(10)" is not correct (it starts with one black and one red.? Not sure where they're from?) Any ideas? Thanks!

Hello, I have come across some unexpected behaviour of the function heatmap in the stats package. This looks like a bug to me, but I might have misunderstood something. When calling the function in symmetric mode, the ColSideColors are plotted correctly, but RowSideColors appear in reverse order. This code (modified from the example on the help page) demonstrates the problem: cU <-

Dear "R-listers" I've been trying to figure out how to annotate charts in ggplot (ie add text to line charts, highlighted boxes etc). By and large, I can get close to what i want with base graphics, but would ideally like to use ggplot whenever possible (additionally, i would like to add text labels automatically to the chart). The code is below I suspect I need to use geom_rect,

I would like to use gridBase to place four separate heatmaps (actually, a stripped-down heatmap.2 from ght gregmisc package that contains only the "image" part) into four different viewports. I can get the placement correct, but I keep 'losing' the previous plot. Any suggestions? Here is some quick example code trying to put a heatmap into the left viewport and then

I am using heatmap with the arguments below. The title size stays the same no matter what I set cex.main to. Is this expected? Can I adjust the title size in heatmap? Also, the position of the main title is at the very upper edge of the output and if I use a "\n" to stack the title the upper line is out of bounds and doesn't show up. I am outputting to pdf. Any help? Thanks,

Hi, I wanted to make more than one side color bar. For example, I can make one side color bar (col1) with the following code: ----------------------------------- library(gplots) mat <- matrix(sample(1:100,40),nrow=5) class1 <- c(rep(0,4),rep(1,4)) col1 <- ifelse(class1 == 0,"blue","red") class2 <- c(rep(1,3),rep(2,5)) col2 <- ifelse(class2 ==

I am in a situation needing 3 ColSideColors for heatmap.2. How can I do that? TIA Daren

Can someone recommend a more sophisticated way to annotate heatmaps than the ColSideColors argument of heatmap and heatmap.2? In particular, I would like to be able to annotate columns with more than one piece of information, like in Figure 1 of the article at http://www3.interscience.wiley.com/cgi-bin/fulltext/117905619/HTMLSTART / doi:10.1002/hep.22256. Some example data and a heatmap:

Hi, i am newbie into ggplot and i thow that i have to learn a lot about this package. I am doing this function to draw an graphic: library(ggplot2) posx <- theme_text(angle=45,hjust=1,face='bold',size=12) posy <- theme_text(angle=0,hjust=1,face='bold',size=12) y1 <- c(1,4,6,1,8,10,6,1,5,4) x <-

Dear HelpeRs, I have a script where I save several thousands of graphics. These are then used in Latex through Sweave. Unfortunately R crashes while making these plots and Windows pops up some message that I run low on virtual memory. I tried to save the plots using pdf(), windows() and postscript() and also tried to run it with R CMD BATCH myscript.R. But after a while R slows down and crashes

Hi, I have thought a lot about my problem and also posted it on stackexchange, the post can be found here: http://stats.stackexchange.com/questions/44276/how-to-plot-3d-gbm but I have got no useful answer, that's why I trry the last possibility, which is to ask you professional guys. I want to recreate the following picture with my own code, the picture can be found in my other post:

To me it seems like writeBin() writes one char/byte more than expected. > con <- file("testbin", "wb") > writeBin("ttccggaa", con) > close(con) > con <- file("testbin", "rb") > readBin(con, what="character") [1] "ttccggaa" > seek(con, what=NA) [1] 9 > close(con) > con <-

Dear list, I have a question on moving color keys when side color bars are added to a heatmap. The R code below produces the color key in the upper left corner. Notice I have added side bars to the heatmap, but how could I move the color key below the image? ------ library(gplots) data(mtcars) x <- as.matrix(mtcars) rc <- rainbow(nrow(x), start=0, end=.3) cc <- rainbow(ncol(x),