search for: ordiellipse

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 <- c("red&...

Hi Users, I am trying to plot 95% confidence ellipses around the 4 groupings found in a PCA ordination and identified a-priori by clustering. I am using ordiellipse to plot the ellipses and it works fine except one of my groups contains only 2 sites and I cannot get an ellipse around them. I'm assuming that 2 points is not enough to perform the relevant calculations here, however I would like to plot one if I could, if only for the sake of pictorial consis...

...green","blue","aquamarine","magenta","yellow")[site.codings] > points(fish.site,pch=21,bg=plotcolor,cex=1.2) #up to this point all works well but when I try to draw the polygons I cant get the lines to colour code the same way as the points did > ordiellipse(graph,site.codings,kind="sd",conf=0.90,draw="polygon") I see there is a command called show.groups but I cant work out how to use it to access the plotcolor file. Any help appreciated. -- Andrew Halford Ph.D Associate Research Scientist Marine Laboratory University of Guam...

Dear Jari Oksanen, I am Trinadh Kumar, a student of Biotechnology from Texas Tech University. I have a question for you regarding constrained ordination graphs. I had previously plotted constrained ordination graphs using distance based redundancy analysis for species data on patients. The species matrix consists of 70 patients and 274 species of bacteria.The metadata matrix consists of 10

...firefactors$comm4 to determine the colors and characters to use in the plot. What I would like to do next is plot the ellipses denoting the 95% confidence intervals of the group centroids, with colors matching those of the points. The following piece of code plots the centroids: with(firefactors, ordiellipse(com.mds, comm4, kind = "se", conf = 0.95, col = as.numeric(firefactors$comm4)), label = TRUE) But the above code makes all of the ellipses blue. Blue is the fourth color in my default palette(), and the first value returned by as.numeric(firefactors$comm4) is 4. I assume that's not...

..."n", xlab="AXIS 1", ylab="AXIS 2") points(vare.cca,display='species') Now, I want to add to this graph a standard error in 'x' and 'y' direction. How can I add it? I tried different options but I do not get it. It will be just like the function ordiellipse of ellipse library and others like ordihull of vegan library, but without add any factor level. The program CAP of Anderson realice this kind of output and I am wondering if in R exists some function implemented that deals with it. Some examples of these graphics will be found in Quero et al., 2008...

Hi!, I made a plot with two variables representing the first two axis of a principle component analysis. My question is: How can I superimpose on such plot an ellipse that represent the 95% interval of confidence of scores? Best regards, Paula -- Lic. Paula Gonzalez Divisi??n Antropolog??a Museo de La Plata. Facultad de Ciencias Naturales y Museo. UNLP. Paseo del Bosque s/n?? - B1900FWA - La

Is there an option to draw concentration ellipses in biplots ? It seems really nice to summarize large number of points of each group. Cheers../ Murli