search for: clusplot

Hello, I have a large data set that has more columns than rows (sample data below). I am trying to perform a partitioning cluster analysis and then plot that using pca. I have tried using CLUSPLOT(), but that only allows for 'princomp' where I need 'prcomp' as I do not want to reduce my columns. Is there a way to edit the CLUSPLOT() code to use 'prcomp', please? # sample of my data PRVID,VAR1,VAR2,VAR3,VAR4,VAR5,VAR6,VAR7,VAR8,VAR9,VAR10,VAR11 PRV1,0,54463,53049,6284...

Dear people, I used clusplot to plot a partition result. The partition result was from pamk with a distance object as input. Then I applied cmdscale on the same distance object for coordinates to make another scatterplot. My problem is this: the coordinates from the cmdscale calculation, though with the same shape, were diffe...

Dear R folk: Perhaps I'm just dense today, but I am having trouble reproducing the principal components plotted and summarized by clusplot. Here is a brief example using the pluton dataset. clusplot reports that the first two principal components explain 99.7% of the variability. But this is not what princomp is reporting. I would greatly appreciate any advice. With best regards, -- Tom > R.version _ pl...

...# listwise deletion of missing mydata <- scale(matrix) # standardize variables fit <- kmeans(mydata, 8) # 8 cluster solution # get cluster means aggregate(mydata,by=list(fit$cluster),FUN=mean) # append cluster assignment mydata <- data.frame(mydata, fit$cluster) library(cluster) clusplot(mydata, fit$cluster, color=TRUE, shade=TRUE, labels=2, lines=0) I get the following error Error in princomp.default(x, scores = TRUE, cor = ncol(x) != 2) : 'princomp' can only be used with more units than variables How can I fix it? Thanks -- View this message in context: http://r....

I created a clusplot from PAM results. It represents how signals have been classified. Signals are identified by a numerical label. My trial distance matrix is made up of 10 rows, one for eacjh signal. I assigned the signals iidentifiers as rownames of the distance matrix. rwn [1] "1104" "1332" &...

I am a relative novice with R and am having some difficulty using 'clusplot' (package Cluster). I have performed PCA analysis (using vegan) on a large set of morphometric measurements and revealed up to 4 principal components. To examine the grouping of the data I have used PAM followed by clusplot to visualise the clusters. My problem is that I would like to see the c...

Hello everyone. I just started learning R for clustering analysis in my research project. I tried k-means method and PAM method, both of which were properly processed with my data. I have some questions about PAM graphical output. Suppose to do the commands shown below; pm<-pam(D, 6) plot(pm) I got two charts after prompted. In the first chart, 6 oval clusters are drawn together

...ot; and "ylab" instead of the default "Component 1" and "Component 2"? When I put "xlab" option in the function, it always says "formal argument "xlab" matched by multiple actual arguments". 2. There seems to be some rotation of the clusplot from the original plot of points. Is there any way to remove this rotation? Any suggestion is appreciated. Haiyong

Dear Friends, require(cluster) x <- rbind(cbind(rnorm(10, 0, 0.5), rnorm(10, 0, 0.5)), cbind(rnorm(15, 5, 0.5), rnorm(15, 5, 0.5))) plot(pp <- pam(x, 2), which.plots = 1) How can I extract the coordinates used in the plot? _____________________________ Professor Michael Kubovy University of Virginia Department of Psychology Postal Address: P.O.Box 400400, Charlottesville, VA 22904-4400

...esponding to the variables (points within an NMR spectrum). I would like to carry out some kind of clustering on these data to see how many clusters are there. I have tried the function clara() from the package cluster. If I use the matrix as is, I can perform the clara analysis but when I call clusplot() I get this error: Error in princomp.default(x, scores = TRUE, cor = ncol(x) != 2) : 'princomp' can only be used with more units than variables Then, I reduce the dimensionality by using the function prcomp(). Then I take the 13 first principal components (80%< variability) and I...

The following code in clusplot.default (package cluster) is in error: x1 <- cmdscale(x, k = 2, eig = TRUE) var.dec <- sum(x1$eig)/sum(diag(x1$x)) if (var.dec < 0) var.dec <- 0 if (var.dec > 1) var.dec <- 1 x1 <- x1$points x1 has components with name...

...m using the cluster package and by the generation of plot.partition I ran into the problem that an alternative title overlaps the default title. > plot.partition(clara.14,which.plot=2,stand=TRUE, main="Silhouette plot of 14 clusters") The manual states that all optional arguments for clusplot.default may also be supplied to plot.partition(). Altering the title in clusplot() works. Question: What am I doing wrong and what would be the correct way to insert the graphic title "Silhouette plot of 14 clusters" alone? I am using R 1.61 on Windows NT and the latest available cluster...

...A 187 163 174 154 30 2 18 6 12 28 50c50 < 2.00 27.25 147.50 114.60 188.50 270.00 16.00 --- > 2.00 27.25 147.50 114.50 188.50 270.00 16.00 OK Running `clara-ex.R' Running `clara.R' Comparing `clara.Rout' to `clara.Rout.save' ...OK Running `clusplot-out.R' Comparing `clusplot-out.Rout' to `clusplot-out.Rout.save' ...26,28c26,28 < [1,] 0.0000 NaN 166.9258 < [2,] NaN 0 NaN < [3,] 166.9258 NaN 0.0000 --- > [1,] 0.0000 NA 166.9258 > [2,] NA 0 NA > [3,] 166.9258 NA 0.0000...

...luster/man/plantTraits.Rd' Warning: /tmp/Rtmpgxd64f/R.INSTALL33128ce7/cluster/man/plantTraits.Rd:69: unexpected END_OF_INPUT 'Structuration de communaut ' *** installing help indices ** building package indices ... ** testing if installed package can be loaded Warning: S3 methods ‘clusplot.default’, ‘clusplot.partition’, ‘pltree.twins’, ‘silhouette.default’, ‘silhouette.clara’, ‘silhouette.partition’, ‘plot.agnes’, ‘plot.diana’, ‘plot.mona’, ‘plot.partition’, ‘plot.silhouette’, ‘print.mona’, ‘print.pam’, ‘print.summary.mona’, ‘print.summary.pam’, ‘print.summary.silhouette’, ‘summary....

...text html latex example animals text html latex example bannerplot text html latex clara text html latex example clara.object text html latex clusplot text html latex clusplot.default text html latex example clusplot.partition text html latex example cluster-internal text html latex daisy text html latex...

First thanks to the fast answer regarding the "Clustplot problem"... Regarding a new problem: for (i in 1:5) { z <- clara(adata, i) plot(z) } in the above code in the plot screen I get something like: clusplot(clara(x=adata,i)) in title in the 2nd type of plot I get silhouete plot of clara(x=adata,k=i,samples=50) How can I pass the real value to the i? What kind of command "transform" a var into their own value ? I tried using something like ~i , %i , but with no luck......

Hi there, Sorry for the double email. Does R have the packages for the following clustering methods? And if it does, what the commands for them? 1. SOM (Self-organization map) 2. Graph partitioning: 3. Neural network 4. Probability Binning Thank you very much! Linda [[alternative HTML version deleted]]

...text file. (refered R-data import -export*.pdf) > read.table("c:\\DataES.txt") V1 V2 1 ACW261 33 2 ACW311 7 3 ACW321 31 4 ACW342 39 5 6 7 Now my question is how do i /*convert text file Data into *.RData* which i can use as a dataset/data.matrix whereby i can use it for clusplot. Thanks in Advance, JJ --- -- Lecturer J. Joshua Thomas KDU College Penang Campus Research Student, University Sains Malaysia [[alternative HTML version deleted]]

...omplete", members=NULL) x<-as.dendrogram(z) plot(x, xlab="mydata complete-LINKAGE", ylim=c(0,4)) #visualization of the dendrogram clusters<-cutree(z, h=1.6) #obtain clusters at cutoff height=1.6 ord<-cmdscale(d, k=2) #Multidimensional scaling of the data down to 2 dimensions clusplot(ord,clusters, color=TRUE, shade=TRUE,labels=4, lines=0) #visualization of the clusters in 2D map var1<-var(clusters==1) #variance of cluster 1 #extract cluster memberships: clids = as.data.frame(clusters) names(clids) = c("id") clids$cdr = row.names(clids) row.names(clids) = c(1:dim(c...

Hi, I have the graph below: | 422 | 1 321 | 1 | 1 |32 1 |23 |_______________________ The numbers are points in coordinates (simplified graph). I need make a cluster analysis of this for identify groups and make a graph with this groups under circle. In R exist several packages for cluster analysis, but, which the package for this analysis and