search for: otus

Hello, I calculate the correlation between two matrices cor(x,y, method="spearman") and I am wondering if it possible to see only the significant correlations. I can do that for single OTUs with cor.test() command but I would like to have an output for whole matrix. Besides,I would like to plot the relative abundance of each OTU, against the number of significant pair-wise correlations to other OTUs. However, I do not know how to introduce p <.05 parameter in the script. Thank you...

I am trying to make the lines thicker in a graph (for a ppt presentation). Here is what I currently have: plot(x,y,type="l", ylab="Number of OTUs", xlab="Number of Samples Collected", col="Black", pch=1, ylim=c(0,6000)) points(x, Sobs$Chao_1_Mean, type="l", col="Gray", pch=1) (this is one of the added lines in the graph). I believe cex can help increase the size of the points. But I haven't...

...rson but I was recommended to use R to perform a nmds plot and PerMANOVA of my dataset. Sample(treatment) in the columns and species (OTU) in the rows. I have 4 treatments (Ambient Temperature, Ambient temperature+Low pH, High temperature, High temperature+low pH), and I have 16 different species (OTUs). Firstly I want to make a nmds plot and see how different the treatments are. Meaning how the species covaries with the environment, I can produce a plot but don't understand how to interpret it and I get an error message. Then I want to make a PerMANOVA analysis comparing the different treat...

...1,112.5,113,100.3,108.2,101.1,104,105.5,106.3) y<-c(110,111,110.2,112.1,119.5,122.1,102,112,112.5,115) xy<-cbind(x,y) library(cluster) UPGMA.orig<-agnes(x) plot(UPGMA.orig,which.plots=2,xlab="",main="",sub="") Look how the dendrogram has been drawn: all the OTUs should line up with 0.0 on the "distance" axis, but it is not the case in the dendrogram obtained here. Is it possible to obtain a traditional dendrogram? (I am using R 2.7.0 with Windows XP) Thanks and best wishes, Marcin

...n OTU table into EstimateS, however, the format of the OTU table has to be changed to fit the format EstimateS will accept. In R, I would like to change the format of the OTU table (from excel). Here is what I need to do, take Example 1 and create Example 2. The problem is that I have hundreds of OTUs, so I can't do this by hand (and I'd love to have a code that I could use for different OTU tables). Thanks! Example 1 Example 2 Species Abundance Species 1 3...

...se a distance matrix as an input for adonis (or any of the other similar hypothesis testing functions) instead of the usual species by sample table. Working in the field of microbial ecology, what I'm trying to do is to overcome the problem of having to use discrete units such as species or OTUs, which are problematic in microbial ecology (if not outright theoretically false). What I have instead is a phylometric distance matrix between all my samples based on a phylogenetic tree. Some people have apparently made such a python implementation <http://qiime.org/scripts/compare_categor...

I am trying to find the percentage of the parameters explaining the bacterial community composition. I have one data matrix with relative abundance of OTUs and one with environmental parameters. I used varpart in vegan package but the values in the venn diagram is bigger than 100% in total.How is it possible? What might be the reason? Thank you library(vegan) gotud <- decostand(gotu,"hell") G.var <- varpart(gotud,~Depth,~CH4_oxidatio...