Hello everybody, I am using the hclust() function in R. I have a 2000*12 matrix of expression data. I have created a distance matrix with dist() using Euclidean method. Then in hclust I have used complete linkage method. Now when I am trying to plot the dendogram with pclust method I cannot see the details of the tree. The gene names and the lower parts of the dendogram are not visible Is there any method by which I can see only selected parts of the dendogram.....or Zoom in or out.... I have used the follwing command for pclust: plclust(H2000, unit = FALSE, level = FALSE, hmin = 0, + square = TRUE, labels =names2000 , plot. = TRUE, + axes = TRUE, frame.plot = FALSE, ann = TRUE, + main = "", sub = NULL, xlab = NULL, ylab = "Height") I am attaching a snapshot of the dendogram that I am getting. Please help ASAP. Thanks in advance, Madhurima. -------------- next part -------------- A non-text attachment was scrubbed... Name: hclust.png Type: image/png Size: 120783 bytes Desc: not available Url : https://stat.ethz.ch/pipermail/bioconductor/attachments/20051108 /d86b7909/hclust.png

Hi, as stated already this is nearly impossible to visualize as a dendrogramm. But you might want to export your data in newick format, I guess it was something like hc2newick or so package "ctc". Then you can visualize the data using standard/specialized treeviewing programs, to explore your trees. But I guess it will be hard to make sense out of such large trees by eye. Cheers, bj?rn > Hello everybody, > > I am using the hclust() function in R. > I have a 2000*12 matrix of expression data. > I have created a distance matrix with dist() using Euclidean method. > Then in hclust I have used complete linkage method. > Now when I am trying to plot the dendogram with pclust method I cannot > see the details of the tree. > The gene names and the lower parts of the dendogram are not visible > Is there any method by which I can see only selected parts of the > dendogram.....or Zoom in or out.... > I have used the follwing command for pclust: > plclust(H2000, unit = FALSE, level = FALSE, hmin = 0, > + square = TRUE, labels =names2000 , plot. = TRUE, > + axes = TRUE, frame.plot = FALSE, ann = TRUE, > + main = "", sub = NULL, xlab = NULL, ylab = "Height") > > I am attaching a snapshot of the dendogram that I am getting. > Please help ASAP. > > Thanks in advance, > Madhurima. > >--------------------------------------------------------------------- --- > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor > >