search for: suparna

...idered with the total no of objects in the row. for example > values[1,2] [1] 0.3611111 and > values[1,] [1] 0.7777778 0.3611111 0.2222222 0.1388889 0.0000000 0.8611111 So there are two numbers more than equals to values[1,2] So > values.new[1,2]= 2/length(values[1,]) With best regard, Suparna ---------------------------- Ms Suparna Mitra Eberhard-Karls-Universität Tübingen Wilhelm-Schickard-Institut Algorithmen der Bioinformatik Sand 14, 72076 Tuebingen Germany Tel. ++49-7071-29 70453 (0) Fax ++49-7071-29 5148 (0) Phone: ++49-176-20361469 (M) ++49-7071-1477169 (R) Alternativ...

...3 4 4 and all the rows represent different species so; > M[1,1] [1] 0.875 ## is the distance value for species 1 for combination data pair 1& 2. Can any body please suggest me what will be the best way to represent these results in plot? Thanks a lot in advance, With best regard, Suparna [[alternative HTML version deleted]]

...87" " 18538" NA NA NA NA NA NA " 262" Main problem is, this code is working for some cases, but not for all. Does any body have an idea, why it is so? Or can anyone show me some other way to do the same. Thanks in advance, With best regard, Suparna [[alternative HTML version deleted]]

Hello R experts, I am having an wired problem to save my RPlot after I use "identify" option. Points are identified properly, but when I try to save that image I get error as: " Error: first argument must be a string (of length 1) or native symbol reference" and the image without identified points are saved. I am having this problem after I upgraded to R version 3.0.0. (Mac).

...matrix above I created by hand to use as a nexus distance matrix data for other methods. So it is better if I can use this distance matrix vector (dist.mat) directly. I couldn't find any package for phylogenetic tree from distance any distance matrix in R. Thank you very much. With best regard, Suparna ---------------------------- [[alternative HTML version deleted]]

Hello, How can I create a symmetric contingency table from two categorical vectors having different length of levels? For example one vector has 98 levels TotalData1$Taxa.1 [1] "Aconoidasida" "Actinobacteria (class)" "Actinopterygii" "Alphaproteobacteria" [5] "Amoebozoa"

Hello, I have a contingency table showing relation between two datasets. I tried to see association among them with the assocplot, but it shows error. mosaicplot of the same data worked perfectly. Can anyone please help me. Con.table=as.matrix(Con.table) > dim(Con.table) [1] 27 27 > assocplot(Con.table,space = 0.3, + main = NULL, xlab = NULL, ylab = NULL) Error in

Hello R experts, I am trying to plot ordiellipse for my data but the col according to factors. Metabolites_raw= read.csv(file.choose(), head = TRUE) #file 21Metabolites.csv Metabolites_t=t(Metabolites_raw[,2:82]) ord <- metaMDS(Metabolites_t, distance="bray") symbol=as.numeric(Metab_metadata$LandType) col.list <-

Dear all, I have one problem to handle a large dataset... It looks like: "read" "no" "length" 2 2 144 7 7 47490 9 9 310944 11 11 10089 14 14 13152 17 17 27363 and so on There are 130000 rows >From this table I need to make a table like 2_1 2 100 2_2 2 44 7_1 7 100 7_2 7 100 ... ... 7_474 7 100 7_475 7 90 9_1 9 100 9_2 9 100 and so on... In words: I want to

...> Does anybody you know why this is happening or how I can model using > the 16 genes? > > I hope anyone could help me with this! > Many thanks in advance, > > Paul > > > [[alternative HTML version deleted]] > > > > > > > > > > From: suparna mitra <suparna.mitra@googlemail.com> > Date: 15 June 2009 7:57:00 PM > To: r-help@r-project.org > Subject: [R] How to build phylogenetic tree by R program from > distance any distance matrix > > > Hello R users, > Can any one please help me to find a way to build p...

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Hello R experts, I am trying to use hmap from package seriation or bertinplot. I have two questions: How can I specify smaller font? I tried with pushViewport(viewport(layout=grid.layout(nrow = 1, ncol = 2), + gp = gpar(fontsize = 8))) but didn't work for the font with bertinplot. Also for hmap I need to arrange the margin so that all the labels are visible. I tried with par(mai=c(3,2,2,2)),

H ello R-experts, I want to do ordination plots using vegan metaMDS. I have a where many cells have zero values. Data structure: X[1:10,1:14] Height.1 Height.2 Height.3 Height.4 Height.5 Height.6 Height.7 Height.8 Height.9 Height.10 Height.11 Height.12 Height.13 D30I1A 46 0 0 0 0 0 0 0 0 0 39 0 98 D30I1B