similar to: heatmap2 error key

Can anybody tell me where to find a copy of heatmap2? I've seen it in my travels across the web but didn't bookmark it and can't find it again. Thanks in advance. Paul `-:-. ,-;"`-:-. ,-;"`-:-. ,-;"`-:-. ,-;"`-:-. ,-;"`-:-. `=`,'=/ `=`,'=/ `=`,'=/ `=`,'=/ `=`,'=/ `=` >==/ >==/

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

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

Hi R users, I'm a quite extensive user of the heatmap() function, and as many others i'm frequently frustrated by its fixed square width / height ratio. Here is a typical example : dev.new() heatmap(matrix(rnorm(1200), nrow=10)) I have a non square matrix to plot with heatmap, as there are many more columns than rows, row labels are larger than necessary but column labels

Hi all, Does anyone know of a fairly easy way to "stretch" a heatmap vertically? I've got 42 arrays and would like to be able to see as many significant genes as possible (right now I can only get 50 genes with it still being readable). In some comparisons there are several hundred significant genes. I've fiddled with the "asp" argument, but that doesn't

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),

Estimados Tengo un problema, R se cuelga (cierra, aborta, etc.) al usar códigos de neuralnet. Copio un ejemplo cualquiera para preguntar si a otros les pasa lo mismo o es un problema puntual en mi computadora (uso R revolution win 10). # install, load package install.packages(NeuralNetTools) library(NeuralNetTools) # create model library(neuralnet) AND <- c(rep(0, 7), 1) OR <- c(0, rep(1,

Hi all, I think the code to calculate the default value of the symbreaks argument in the gplots::heatmap.2 function is wrong. The documentation says symbreaks defaults to true if any negative values are detected in the data passed in. The relevant code in the parameter list of this function definition (gplots 2.7.3) is this: symbreaks = min(x < 0, na.rm = TRUE) || scale !=

The following code: res <- gsub("(*UCP)\\b(i)\\b", "", "nhgrimelanomaclass", perl = TRUE) results in: Error in gsub(sprintf("(*UCP)\\b(%s)\\b", "i"), "", "nhgrimelanomaclass", : invalid regular expression '(*UCP)\b(i)\b' In addition: Warning message: In gsub(sprintf("(*UCP)\\b(%s)\\b",

R CMD build fails with recent R-devel because it is looking for texi2dvi in /usr/local/bin, but on this system, MacTex has installed it in /usr/bin. $ R CMD build IRanges * checking for file 'IRanges/DESCRIPTION' ... OK * preparing 'IRanges': * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes * creating vignettes ... ERROR

On 07/06/2015 9:14 PM, Dirk Eddelbuettel wrote: > > On 7 June 2015 at 20:46, Duncan Murdoch wrote: > | I am seeing very strange behaviour in R 3.2.0 patched (r68272) and a new > | build of R-devel. The sessioninfo() from the former is below. > | > | Here's what I see: If I set the locale, and trigger a namespace load, a > | version comparison gives NA, and I get an

Hello, I don't know if the problem originates from R-devel 3.2 or Rcurl itself. I post this message to the R-devel list and to the author of RCurl (duncan at r-project.org). > library("RCurl") Le chargement a n?cessit? le package : bitops > print(sessionInfo()) R Under development (unstable) (2015-02-03 r67717) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under:

Hi, I wonder if this is expected or I'm doing a wrong thing. pdf() dev.control('enable') library("grid") plot(1) grid.text("A") res = recordPlot() dev.off() cairo_pdf() replayPlot(res) dev.off() *** caught segfault *** address 0x4, cause 'memory not mapped' > sessionInfo() R version 3.3.2 (2016-10-31) Platform: x86_64-apple-darwin13.4.0 (64-bit)

Muchas gracias Carlos. Tengo las mismas versiones pero no logro separar los chunks cuando uso #+, pero si lo logro cuando uso #". Mi script es spin("prueba.R", knit = FALSE) y si me hace un Rmd. #+ a = c(1,2,3) #+ mean(a) Ejecuto, > spin("prueba.R", knit = FALSE) y obtengo un prueba.Rmd ```{r } a = c(1,2,3) ```{r } mean(a) ``` Pero si escribo: #' a =

Muchas gracias Carlos. Tengo la versión de knitr 1.14 Corrí el ejemplo que me dices y resulta en lo mismo, no se crean chunks diferentes. Parece que para separar chunks se debe incluir #' Por ejemplo, estas 2 líneas de códigos del ejemplo: #+ test-chisq5 sum(x^2) # chi-square distribution with df 5 #+ test-chisq4 sum((x - mean(x))^2) # df is 4 now Dan como resultado en el Rmd (todo queda

Hello, All: Try the following: par(bg='transparent') plot(1:3) I get two plots superimposed, one over twice the size it should be, much of it outside the device region. Thanks for all you do to make R such a useful tool. People all over the world live better today, because R helps improve the effectiveness of data analysts. Spencer Graves >

Hello: In plot.ts, las=1 applies to ylab and not axis labels with multiple series. The documented behavior is to have las=1 apply to axis labels and not ylab. To see this, please try the following: plot.ts(1:4, las=1) plot.ts(matrix(1:8, 4), las=1) On my Mac, the second displays behavior I did not expect. If I've done something stupid here, please advise;

Hi! I just started this course and just installed R and RStudio but I got this warning/error messages when I open R and RStudio: During startup - Warning messages: 1: Setting LC_CTYPE failed, using "C" 2: Setting LC_COLLATE failed, using "C" 3: Setting LC_TIME failed, using "C" 4: Setting LC_MESSAGES failed, using "C" 5: Setting LC_MONETARY failed,

Hi, The `quietly` argument of `require` is documented as follows: quietly: a logical. If ?TRUE?, no message confirming package attaching is printed, and most often, no errors/warnings are printed if package attaching fails. However: > require(foo, quietly=TRUE) Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :

Hello: A call to help(..., help_type='text') fails with "package='fda": > install.packages('fda') > help(package='fda', help_type='text') Error in formatDL(nm, txt, indent = max(nchar(nm, "w")) + 3) : incorrect values of 'indent' and 'width' I have this wrapped inside "try" in