search for: gclus

...I have a matrix of M-values. I do the following. #The distance between the columns. sampdist <- dist(t(matrix[,]), method="euclidean") sclus <- hclust(sampdist, method="average") #The distance between the rows. genedist <- dist(matrix[,], method="euclidean") gclus <- hclust(genedist, method="average") heatmap(matrix[,],Rowv=as.dendrogram(gclus),Colv=as.dendrogram(sclus), col=rbg) So far so good. But what if I want to look at a group of genes that appear to have the same expression pattern in the heatmap? How do I zoom in on a dendogram in a h...

Hello, I am relatively new to R and I am working through the code that is provided in the book Numerical Ecology with R and I have run across an error message that I can't seem to figure out. I am using the vegan, ade4, gclus and cluster packages. The code is as follows: # Ordered community table # Species are ordered by their weighted averages on site scores or <- vegemite(spe, spe.chwo) spe is the dataframe spe.chwo came from: spe.norm <- decostand(spe, "normalize") spe.ch <- vegdist(spe.norm,...

> Date: Mon, 20 Feb 2006 16:43:55 -0600 > From: Aldi Kraja <aldi at wustl.edu> > > Hi, > Using package gclus in R, I have created some graphs that show the > trends within subgroups of data and correlations among 9 variables (v1-v9). > Being interested for more details on these data I have produced also the > var-covar matrices. > Question: From a pair of two subsets of data (with 9 variables...

Hi, Using package gclus in R, I have created some graphs that show the trends within subgroups of data and correlations among 9 variables (v1-v9). Being interested for more details on these data I have produced also the var-covar matrices. Question: From a pair of two subsets of data (with 9 variables each, I have two...

...39;, 'fNonlinear', 'fOptions',   'forecast', 'foreign', 'fpc', 'fracdiff', 'fRegression', 'FrF2', 'FrF2.catlg128', 'fTrading',   'fUnitRoots', 'gamlss', 'gamlss.data', 'gamlss.dist', 'gclus', 'gdata', 'geoR', 'GGally', 'ggm',   'ggplot2', 'gmodels', 'gridBase', 'gWidgets', 'gWidgetstcltk', 'HH', 'Hmisc', 'httr', 'igraph',   'igraph0', 'inline', 'ipred', &...

...39;cubature' 'kinship' 'gam' 'tripack' 'akima' 'logspline' 'gplots' 'maxLik' 'miscTools' 'sem' 'rgdal' 'network' 'numDeriv' 'statnet' 'rgenoud' 'hexbin' 'ellipse' 'gclus' 'mlbench' 'randomForest' 'SparseM' 'Formula' 'ineq' 'mlogit' 'np' 'plm' 'pscl' 'quantreg' 'ROCR' 'sampleSelection' 'scatterplot3d' 'systemfit' 'truncreg' 'urca' '...

...ames. or also hclust -> as.dendrogram -> cut -> .. -> [[ -> Note that there also is reorder.dendrogram() for reordering dendrogram nodes ``sensibly'' --- something that heatmap() does, but you can play with quite a bit. Further, note Catherine Hurley's "gclus" package which orders/reorders 'hclust' objects directly, but with a more interesting algorithm. Note that I'd strongly recommend to use R 1.9.1 beta for these, since I know which bugs in the dendrogram code I have fixed since R 1.9.0... michael> An important message to t...

...I am trying to plot a matrix of m-values in a heatmap Johan> with "average linkage". The rows are M-values of Johan> genes and the columns are my slides. I do the Johan> following and get the following error message: >> heatmap(Matrix[,],Rowv=as.dendrogram(gclus),Colv=as.dendrogram(sclus),col=rbg) Johan> Error in match.fun(FUN) : evaluation is Johan> nested too deeply: infinite recursion? Error: Johan> evaluation is nested too deeply: infinite recursion? The problem happens when trying to plot a large dendrogram. The "dendroga...

Hello everyone, I am currently using the mvpart package and would like to change the color scheme it uses, and was hoping someone could help me out. All of the papers I have found have used a grayscale but I can't seem to figure out how they did that! Currently, mvpart plots barplots in a repeating sequence of 3 shades of blue. So if you have 6 response variables the same shade of blue is used

I'm running R 2.9.2 build 5464 on OS X 10.5.8. Having encountered memory allocation problems, I ran the problematic code in R64, the 64- bit version of the same build. When I attempt to load openNLP I receive the error message that the 32-bit version that I had been using does not run in R64. Assuming there is a 64-bit version, can I install and load it in R64 and, when I

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...(0.3.0), frailtypack (2.2-14), FrF2 (1.1-3), frontier (0.996-8), ftsa (1.9), FunNet (1.00-9), gamlss (4.0-0), gamlss.add (4.0-0), gamlss.cens (4.0.0), gamlss.data (4.0-0), gamlss.dist (4.0-0), gamlss.mx (4.0-0), gamlss.nl (4.0-0), gamlss.tr (4.0-0), gamlss.util (4.0-0), gap (1.0-23), gbm (1.6-3.1), gclus (1.3), gdata (2.8.0), geoR (1.6-28), geoRglm (0.8-28), geosphere (1.2-4), geozoo (0.4.1), GExMap (1.1), ggplot2 (0.8.8), ghyp (1.5.3), glmnet (1.4), gmm (1.3-2), gplots (2.8.0), gputools (0.21), gRain (0.8.5), grImport (0.6-1), gss (1.1-5), gsubfn (0.5-3), gtools (2.6.2), gWidgets (0.0-41), gWidget...