similar to: multiple annotations on a heatmap

I'm able to do this as follows, but am wondering if anyone knows a simpler way which still avoids explicit loops? > (mystring <- letters[1:5]) [1] "a" "b" "c" "d" "e" > unlist(sapply(mystring[-length(mystring)], + function(x) paste(x,mystring[(grep(x,mystring)+1):length(mystring)],sep=""))) a1 a2 a3

The order() function allows you to specify multiple vectors, which are used successively to break ties. If I want to use many vectors to break ties (say, 25 or more), that are columns of a matrix or elements of a list, does anyone know a shortcut to do this without passing 25 arguments to order()? -- Levi Waldron post-doctoral fellow Jurisica Lab, Ontario Cancer Institute Division of Signaling

For example, subtracting 1:2 from the rows of a two-column matrix: > t(apply(matrix(1:6,ncol=2),MARGIN=1,function(y) y - 1:2)) [,1] [,2] [1,] 0 2 [2,] 1 3 [3,] 2 4 > sweep(matrix(1:6,ncol=2),MARGIN=2,1:2,FUN="-") [,1] [,2] [1,] 0 2 [2,] 1 3 [3,] 2 4 Is there a logic to this difference, or is it just a quirk of the history of these

How can I look up the aspect ratio of a plot, so I can use that to correctly adjust the angle of text which is supposed to be parallel to a line in the plot? The following example code works for a 1:1 aspect ratio, but puts the text at the wrong angle if the plot region is short and wide or tall and narrow. I can't find a par() component containing the plot aspect ratio. It will be for

Hi STATISTICA has a function called "Two-way joining" (see http://www.statsoft.com/TEXTBOOK/stcluan.html#twotwo) and the reference material states that this is based on the method as published by Hartigan (found this paper: http://www.jstor.org/pss/2284710 through wikipedia). What is the relationship (if any) between the "heatmap" function in R and this technique? Is there an

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 R users, I have various vector geometry operations to perform on 3-D coordinate data located on multiple (500+) csv files. The code I have written for the calculations works just fine. I have written a 'for' loop to automate the task of extracting the coordinates from the files and perform the analyses. The loop works reasonable well, but if the number of csv files is greater than

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 <-

Hello dear R help, The motivation for my question is wanting to run HTMLStart {R2HTML package} from "source". *Background:* I was happy to discover the [ HTMLStart/HTMLStop, HTMLplot] functions in the R2HTML package. They allow my R code to run almost as is, but while writing most of the output (including the figures, when using HTMLplot) into an external HTML file. This method

Hi All, I've been having a little trouble using R2HTML and a loop, but can't figure out where the problem lies, any hints gratefully received. My code at the minute, (Which does work) is in the following: library(R2HTML) HTMLStart(outdir = file.path("C://Example_work","R_projects","Dynamic_creative"),filename = "RMDC_mockup",Title="Mock up for

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,

Im developing an application with R and Gtk+. It's just a simple GUI which helps new users to interactuate with R. Thing is, when you do a statistical analysis, I also want to provide a HTML report, but HTMLStart doesnt work propperly when executing from TinnR. It does create the file but not empty, I've tried some examples from different websites, and it's always the same.. it works

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

I am using attributes colsep and sepwidth from heatmap.2 function, however when using larger values for sepwidth the following columns are not moved to the right but the seperator is covering the column(s) with a white bar and the column labels and ColSideColors remain at their positions, is this intended? I expected the following columns to be shifted to the right by sepwidth. Is there a way

Hi, I am trying to prepare a report with R2HTML using HTMLStart(outdir="./html", filename="report", echo=T, HTMLframe=F) then, for instance, I want to get the output of a loop: for (i in 1:20) print(summary(rnorm(1000))) but only the first of summaries really ends up in the html file. What am I doing wrongly? Thanks, Werner

Hello, I''m using R2HTML library to make a HTML page output (both data frames and graphics): HTMLStart(outdir=paste(getwd(),"/prove html", sep = ""),filename="index", echo = F, HTMLframe = T, withprompt = "HTML> ", CSSFile = "R2HTML.CSS", Title = "Indici di attivit?") ...

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),

Here I am again with question I'll feel foolish for asking, when I see the answer. I'm trying to produce a report and here's where I get stuck: How do I get R2HTML to produce the same number format? Particularly remove the decimal places for Par and Sal. Are there better methods to produce this type of report? Thanks, L.A. R version 2.10.0 XP