similar to: plotting issues with PCA

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 <-

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

Hello, R-Help - I am trying to plot the results of an ordination from package vegan. The tricky part for me right now is getting the colors of the ellipses denoting the 95% confidence intervals of the group centroids to match the colors of the points for those same groups. >From and earlier post, I saw the code to make a plot of the ordination using different colors for my different groups.

I'm new to making bubble plots with R, so I was going to try the following: https://stat.ethz.ch/pipermail/r-sig-geo/2009-August/006258.html Unfortunately, it looks like rgdal is not part of 2.14.  I'm not sure if it was the mirror I selected or something else is going on. > install.packages("rgdal") --- Please select a CRAN mirror for use in this session --- Warning

Dear all, I realised a correspondence analysis with function cca() of vegan library. Just like in Okansen (2010) in the example of R help: library(vegan) data(varespec) data(varechem) vare.cca<-cca(varespec~ Al + P + K, varechem) With plot.cca() function I represented the species matrix in the next way: plot(vare.cca,display="species") Being similar to: plot((c(-2,2)),(c(-2,2)),

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

Hello, I do have two different time series A and B, they are different in length and starting point. A starts in Jan, 2012 and ends in Dec, 2012 and B starts in March, 2012 and ends in Nov, 2012. How can I plot those two series A and B in the same plot? I.E., from Jan. 2012 - Feb, 2012, it would have one data point from A and from Mar, 2012-Nov, 2012, it would have two data points from A and B,

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