search for: distfun

Dear R wizards, Hopeful someone can help me with what I believe is a pretty simple task. I pretty new to R so some (much) of the obvious escapes me. How do I get a distance matrix into heatmap? What do I tell distfun if what I'm trying to map is already an ordered distance matrix? I tried >heatmap(x, distfun=as.dist(x)) where x is the distance matrix but R gave me an error. Thanks in advance for any help. Paul Lepp `-:-. ,-;"`-:-. ,-;"`-:-. ,-;"`-:-. ,-;"`-:-. ,-;"`...

...ramming language book (perhaps I should invest in it) and the online help wasn't that helpful to me, so I would very much appreciate any responses y'all may have. Thank you very much, --Avi ##################################################### Code (Unfinished) MSEFit <- function (x, distfun, start, ...) { require (MASS); require (actuar); Call <- match.call(expand.dots = TRUE) if (missing(start)) start <- NULL dots <- names(list(...)) if (missing(x) || length(x) == 0L || mode(x) != "numeric") stop("'x' must be a non-...

...was reversed in the two functions (but all individual columns were grouped correctly). Looking through the code for heatmap as a most definite nonexpert, it seems to me that hclust is also invoked by heatmap. > heatmap function (x, Rowv = NULL, Colv = if (symm) "Rowv" else NULL, distfun = dist, hclustfun = hclust, add.expr, symm = FALSE, ... hcr <- hclustfun(distfun(x)) ddr <- as.dendrogram(hcr) .... hcc <- hclustfun(distfun(if (symm) x else t(x))) ddc <- as.dendrogram(hcc) I understand it is possible to add Rowv...

...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 <- cor(USJudgeRatings) sideCols <- rainbow(ncol(cU)) heatmap(cU, symm = TRUE, distfun = function(c) as.dist(1 - c), ColSideColors=sideCols, RowSideColors=sideCols) Reversing the RowSideColors argument does not solve the problem: heatmap(cU, symm = TRUE, distfun = function(c) as.dist(1 - c), ColSideColors=sideCols, RowSideColors=rev(sideCols)) I had a look at the the...

Hi, Could you please help? Heatmap doesn't work with: > heatmap(as.matrix(SPIV2),na.rm = T) Error in hclustfun(distfun(x)) : NA/NaN/Inf in foreign function call (arg 11) There are no 0 data rows or column Thanks a lot Regards --------------------------------------- David

...MDS( X ="bray") Square root transformation Wisconsin double standardization Error in if (any(dist < -sqrt(.Machine$double.eps))) warning("some dissimilarities are negative -- is this intentional?") : missing value where TRUE/FALSE needed In addition: Warning messages: 1: In distfun(comm, method = distance, ...) : you have empty rows: their dissimilarities may be meaningless in method “bray” 2: In distfun(comm, method = distance, ...) : missing values in results I realised some of the values are either zero or similar. I tried to check it with distance X .dist <- metaMD...

Hi, I am having troubles with heatmap(). I have a matrix containing pairwise distance values and I want to plot this matrix with heatmap. I wonder now what distfun is for. Is a distance matrix computed from my initial matrix again and then plotted? cheers, andreas

Hi netters, I have a matrix X of the size (1000,100). The values are from -3 to +3. When I tried heatmap(X, distfun=function(c),dist(c,method="bin"),hclustfun=function(m),hclust(m,method="average")) I got the error message: Error: evaluation nested too deeply: infinite recursion / options(expressions=)? However, if I used default parameters for distfunction: heatmap(X, hclustfun=function...

...;stepfun", class(rval)) attr(rval, "call") <- sys.call() rval } and as a particular example, to see how the E.C.D.F. behaves in the length--biased framework consider running the following function with different values for n lengthBiasExample <- function(n=100) { distFun <- function(x) pgamma(x,shape=1,rate=1) ##lenght biased version of a gamma(shape=1,rate=1) x <- rgamma(n,shape=2,rate=1) par(ask=T) Fx <- ecdf(x) newFx <- newEcdf(x,1/x) plot(Fx,pch="+") curve(distFun,from=0,to=10,add=T,col="red") plot(newFx,pch="+&q...

...ot;) n <- length(x) if (is.character(densfun)) { distname <- tolower(densfun) densfun <- switch(distname,exponential = dexp,gamma = dgamma, "log-normal" = dlnorm, lognormal = dlnorm, weibull = dweibull, pareto = dpareto, NULL) distfun <- switch(distname,exponential = pexp,gamma = pgamma, "log-normal" = plnorm, lognormal = plnorm, weibull = pweibull, pareto = ppareto, NULL) if (is.null(densfun)) stop("unsupported distribution") if (distname %in% c("l...

...ucket <- 10 # numero de buckets >> >> # Generamos la muestra de tamaño n >> sample <- sort(rlnorm(n, meanlog = mean, sdlog = sd)) >> # Función de distribución >> df <- plnorm(sample, meanlog = mean, sdlog = sd) >> lognorm1 <- data.frame(sample=sample, distfun=df) >> # Gráfica de la función de distribución sin bucketizar >> plot(lognorm1, type = "l", col = "red") >> >> # Bucketización - Muestra bucketizada >> library(plyr) >> dt <- data.frame(sample=sample, bucket=rep(1:nbucket, each = n/nbucket)...

Hi all, The function heatmap uses the functions dist and hclust with default parameters. How to change these parameters? For example, i want to use the ward criterion for hierarchical clustering with binary distance. Best regards, Olivier.

Hi, I run into following error when using heatmap() for data matrix "xx". Any help is appreciated? "xx" contains many "NA"s. > hv <- heatmap(data.matrix(xx)) Error in hclustfun(distfun(if (symm) x else t(x))) : NA/NaN/Inf in foreign function call (arg 11) Thanks a lot. Yuhong ********************************************************* THIS ELECTRONIC MAIL MESSAGE AND ANY ATTACHMENT IS CONFIDENTIAL AND MAY CONTAIN LEGALLY PRIVILEGED INFORMATION INTENDED ONLY F...

Hi - If I have a hypothetical distribution as an array distribution<-c(0,1,2,3,4,5,6,7,8,9) and I want to find the probability there is a value smaller than a new value. new_value<-4 (such that I'd get this type of output) new_value p-value 4 0.5 3.4 0.4 3 0.4 0 0.1 -1 0.0 Thanks for the help, I bet this is really easy... :/ Stephen -- The Wellcome Trust Sanger Institute is

heatmap.2 defaults to dist for calculating the distance matrix and hclust for clustering. Does anyone now how I can set dist to use the euclidean method and hclust to use the centroid method? I provided a compilable sample code bellow. I tried: distfun = dist(method = "euclidean"), but that doesn't work. Any ideas? library("gplots") library("RColorBrewer") test <- matrix(c(79,38.6,30.2,10.8,22, 81,37.7,28.4,9.7,19.9, 82,36.2,26.8,9.8,20.9, 74,29.9,17.2,6.1,13.9, 81,37.4,20.5,6.7,14.6),ncol=5,byrow=TRUE) col...

...est) <- c("Exp1","Exp2","Exp3","Exp4") rownames(test) <- c("Gene1","Gene2","Gene3", "Gene4") test <- as.table(test) mat = data.matrix(test) heatmap.2(mat, dendrogram="row", Rowv=TRUE, Colv=FALSE, distfun = function(x) dist(x,method = ''maximum''), hclustfun = function(x) hclust(x,method = ''centroid''), xlab = NULL, ylab = NULL, key=TRUE, keysize=1, trace="none", density.info=c("none"), margins=c(6, 12), col=bluered ) This gives a...

...quot;) # Arbitrarily assigning NA to some elements mtcars[2,2] <- "NA" mtcars[6,7] <- "NA" mydata <- mtcars hclustfunc <- function(x) hclust(x, method="complete") # Initially I wanted to use this but it didn't take NA #distfunc <- function(x) dist(x,method="euclidean") # Try using daisy GOWER function # which suppose to work with NA value distfunc <- function(x) daisy(x,metric="gower") d <- distfunc(mydata) fit <- hclustfunc(d) # Perform clustering heatmap he...

...erates the dissimilarity index for island. (Does it compare species presence/absence between a pair of island? Should the two islands be specifically located or close to each other?) Thank you Elaine Code # NMDS library(MASS) library(vegan) island.NMDS <- metaMDS(island,k=2, distfun = betadiver, distance = "sim",trymax=100,zerodist="add") plot(island.NMDS, type = "n") #Simpson Dissimilarity Index library(betapart) island.dist<-beta.pair(island, index.family="sor") class(island.dist) [[alternative HTML version del...

Hello R-user community! I am running R 2.7.0 on a Power Book (Tiger). (I am still R and statistics beginner) Presently I try to run the function metaMDS (vegan) using an existing dissimilarity-matrix. As I would like to start with this matrix I thought I could just give the matrix using the x= -argument Test<-metaMDS(x=Dist.Gower) Fehler in inherits(comm, "dist") :

Hi, I am using heatmap.2 of gplots to make heatmaps of my the attached file. I am giving my code for the same .. library(gplots) x=read.table("1.txt", header=TRUE) mat=data.matrix(x) heatmap.2(mat, col=greenred(75), Rowv=TRUE, Colv=TRUE, distfun = dist, hclustfun = hclust, dendrogram = c("both"), scale = c("row"), na.rm=TRUE, trace="none", sepwidth=c(0.05,0.05), margins = c(5, 10), xlab = "EXPRESSIONS", ylab = "GENES", labRow = NULL, labCol = NULL, key=TRUE, keysize=1, density.info=c("...