similar to: Plotting Ellipses and Points of Matching Colors in an Ordination

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 <-

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

Hi Listers, This has a simple answer but it has been eluding me nonetheless. I have been building a PCA plot from scratch with the ability to plot predefined groups in different colors. This has worked fine but when I try to get a polygon drawn around each of the groups it is not recognising my colour file correctly and is only printing the first colour in the file....code is below

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, I've got a small dataset on box turtle shell measurements that I would like to perform a detrended correspondence analysis on. I thought that it would be interesting to examine the morphometrics for each species in the area of overlap and in areas where neither species occurs.  I've taken a look at the dune and dune.env datasets in vegan. Using the str() command gives me  >

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

Hi R-Help - If I make a plot: numYears = 500 plot(x = c(1,numYears), y = c(200,300), xlab = "Time", ylab = "Vegetation Class", xlim = c(100,600), ylim = c(200,300), type="n") Is there a way to make different parts of the background for the plot different colors? For example, I'd like to have the background color col = (250,250,0,50) for y = c(200,204), and col

Greetings Everyone - I have a data frame "x" that looks like this: v1 v2 1 A 1 B 1 B 2 B 2 W 2 W 3 D 3 D 3 Z What I would like to do is create a new data frame, "y", that has one row for each unique value of v1, and returns the corresponding mode of v2. If I were to run it on the above data frame, it should therefore return: v1 v2 1

Hello R Help! I would like to make a legible boxplot of tree growth rates for each of seven tree species at each of seven different sites. It's a lot of data to put on one figure, I know. I made a beautiful, interpretable figure using color, but my target journal can't deal with color figures. I can use seven shades of grey to fill the boxes, but the figure then becomes uninterpretable -

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

Hi Im currently trying to plot my NMDS data together with fitted variables (envfit funct) on an ordination plot. The plot function shows two displays="sites" and "sp". I was wondering how to plot it so that the sites come up as different points for different sites but the species come up as actual names? It looks a little busy at the moment with everything in. Sya -- View

Hello, I am trying to learn how to do PCA. I found a tutorial online, but what I'm seeing in my installation does not match what is in the tutorial. Specifically, if I select Statistics:Dimensional Analysis: Principal-components analysis, the dialog I am presented with does not include an option to create an ordination plot. My question is why not? Is this a problem with my data set,

I am severely rusty re. multivariate / ordination analysis, having done my last work 40 years ago (in plant ecology). I am interested in exploring applications of multivariate analytic approaches to data from the history of motion picture films. I'd very much appreciate any pointers as to possibly appropriate proceedures. The individual "samples" may be individual films and the

A rather strange situation here and I've not found the source of the problem. The point is to print a ternary plot matrix of compositional data with ellipses enclosing 95% of the variance in each plot. The ellipses display on the monitor, dev = x11cairo (see attached winters-x11cairo.pdf), but not when sent directly to a file, dev = pdf (see attached winters-pdf.pdf). Here's

Dear R Users: What I need to do is to plot two ellipses in the same graph (one for each group). You can use either X1 or X2 as the X-axis and the other variable as the Y-axis. Also I need to show the 95% C.I. or P.I. of the overlapping part of the two ellipses, and for each ellipse separately. Data can be found at http://www.usm.maine.edu/~aaboueissa/Rhelps/dataelipse.txt Thank you so

Hi, I have read your post about plotting multiple CI ellipses and I would like too, but I don?t know how. I would like to plot an ellipse for each group and I have slope and intercepts, but I don?t know what to put in the arguments shape and radius. CAn you help me please?

hello, sorry for posting what may be a simple question: i do have a matrix of coordinates (positional judgments, see below) and now want to calculate and plot the corresponding error ellipse. can anyone help me with the exact steps/syntax? > xyDat X Y 1 -0.49 -2.13 2 0.91 0.48 3 0.20 -2.80 4 -0.76 -3.23 5 -0.36 2.50 6 1.38 1.24 7

hi, i am using this script on our webserver to plot data / draw ellipses for a flex movie... would like to add the areas of the ellipses to another legend just like the means for the distance. the data looks like: x (dispersion), y (distance), Club (name of the club for grouping) thanks, sam ## usage: Rscript nikeScatter.R infile outfile level1 level2 minX maxX minY maxY ## load

Hello, I'm developing an ordination using metaMDS (package vegan). The analysis identifies 3 distinct groups that I'd like to define by either adding circles or ellipses to help identify the groups. The data set is a spatial temporal data base depicting change in each of 4 areas over 3 time periods. I can add lines that would link each of the time - x - area trajectories, but