I have the following data: gene_name microarray expression A 2323 B 1983 .... ..... I have about 10,000 observations. I would like to know if there is a way to create an interactive plot.. Mainly one that shows all the points, but when a point is clicked on it shows what gene_name it is If not, does anyone recommend another way to output a plot (using maybe bioconducter bc this is microarray expression) that is informative about the gene_names.
mark salsburg <mark.salsburg at gmail.com> wrote: [...]> Mainly one that shows all the points, but when a point is clicked on > it shows what gene_name it isI think ?identify will help you. -- Sebastian P. Luque
Hi R users and developers: I want to know how can I save memory in R for example: - saving on disk a matrix. - using again the matrix (changing their values) - saving again the matrix on disk in a different file. The idea is that I have a process that generate several matrices, but if I keep them all in memory it will overflow. How can I save them in different files, so I use the same amount of memory for each processed matrix? Thank you for your help. -- Kenneth Roy Cabrera Torres Universidad Nacional de Colombia Sede Medellin Tel 430 9351 Cel 315 504 9339
What kinds of matrices? There are facilities in the Matrix and SparseM packages that might help for sparse matrices. If they are N x k where N is large and k is not, can you compute something like the QR decomposition and get away with keeping only the R part for most of your matrices? One could potentially define a class of matrices that are only kept in memory only when needed; I think S-Plus may do that. It would take a lot of work to make that work generally, but you might be able to accomplish what you need with a much smaller effort. spencer graves Kenneth Roy Cabrera Torres wrote:> Hi R users and developers: > > I want to know how can I save memory in R > for example: > - saving on disk a matrix. > - using again the matrix (changing their values) > - saving again the matrix on disk in a different file. > > The idea is that I have a process that generate several > matrices, but if I keep them all in memory it will overflow. > > How can I save them in different files, so I use the same > amount of memory for each processed matrix? > > Thank you for your help. >-- Spencer Graves, PhD Senior Development Engineer PDF Solutions, Inc. 333 West San Carlos Street Suite 700 San Jose, CA 95110, USA spencer.graves at pdf.com www.pdf.com <http://www.pdf.com> Tel: 408-938-4420 Fax: 408-280-7915
Thank you Dr. Spencer Graves for your answer. What kind of matrices? They come form an image of about 3000x5000, and I need to generate arround 1024 matrices of the same size, they are not sparse matrices. What function can I use to, once generated one matrix, I could save into disk and then use the same space for the following, and so on. Thank you very much for your help Kenneth Spencer Graves wrote:> What kinds of matrices? There are facilities in the Matrix and >SparseM packages that might help for sparse matrices. If they are N x k >where N is large and k is not, can you compute something like the QR >decomposition and get away with keeping only the R part for most of your >matrices? > > One could potentially define a class of matrices that are only kept >in memory only when needed; I think S-Plus may do that. It would take >a lot of work to make that work generally, but you might be able to >accomplish what you need with a much smaller effort. > > spencer graves > >Kenneth Roy Cabrera Torres wrote: > > > >>Hi R users and developers: >> >>I want to know how can I save memory in R >>for example: >> - saving on disk a matrix. >> - using again the matrix (changing their values) >> - saving again the matrix on disk in a different file. >> >>The idea is that I have a process that generate several >>matrices, but if I keep them all in memory it will overflow. >> >>How can I save them in different files, so I use the same >>amount of memory for each processed matrix? >> >>Thank you for your help. >> >> >> > > >
On Thu, 14 Jul 2005, Kenneth Cabrera wrote:> Thank you Dr. Spencer Graves for your answer. > > What kind of matrices? They come form an image of about 3000x5000, and > I need to generate arround 1024 matrices of the same size, they are not > sparse > matrices. > > What function can I use to, once generated one matrix, I could save into disk > and then use the same space for the following, and so on.You can use either save or .saveRDS/serialize followed by rm() and gc(). You cannot use the same space, but you can free up the space. Then when you need the data again, load/.readRDS/unserialize can pull the object back. (If you arrange this right the object will only go into a temporary frame and so only be needed one at a time.)> > Thank you very much for your help > > Kenneth > > Spencer Graves wrote: > >> What kinds of matrices? There are facilities in the Matrix and >> SparseM packages that might help for sparse matrices. If they are N x k >> where N is large and k is not, can you compute something like the QR >> decomposition and get away with keeping only the R part for most of your >> matrices? >> >> One could potentially define a class of matrices that are only kept >> in memory only when needed; I think S-Plus may do that. It would take a >> lot of work to make that work generally, but you might be able to >> accomplish what you need with a much smaller effort. >> >> spencer graves >> >> Kenneth Roy Cabrera Torres wrote: >> >> >>> Hi R users and developers: >>> >>> I want to know how can I save memory in R >>> for example: >>> - saving on disk a matrix. >>> - using again the matrix (changing their values) >>> - saving again the matrix on disk in a different file. >>> >>> The idea is that I have a process that generate several >>> matrices, but if I keep them all in memory it will overflow. >>> >>> How can I save them in different files, so I use the same >>> amount of memory for each processed matrix? >>> >>> Thank you for your help. >>> >>> >> >> >-- Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595