I would like to plot vectors from a capscale ordination using VEGAN.
I am familiar with the display ="bp" command, but this adds labels that are obscured by site points. Is there an easy means of removing these? I am happy to add them in later i.e. once exported and within word for publication.
My code thus far is as follows:
plot(mod, scaling = 3, type="n")
with(data, points(mod, display="sites", cex=Pointsize,
pch=ifelse(Cat=="Reference",21,19)) ,bg=Cat,)
with(data,text(mod,display="bp"))
Help will be appreciated
Use the points() method instead of the text() method:
points(mod, display = "bp")
(There also should be no need for the with(data) in that last line of code you show.)
Here is a reproducible example:
require(vegan)
data(varespec)
data(varechem)
ord <- cca(varespec ~ ., data = varechem)
plot(ord, type = "n", display = "sites")
points(ord, display = "sites")
points(ord, display = "bp")
Related
I am trying to plot the GMM of my dataset using the Mclust package in R. While the plotting is a success, I do not want points to show in the final plot, just the ellipses. For a reference, here is the plot I have obtained:
GMM Plot
But, I want the resulting plot to have only the ellipses, something like this:
GMM desired plot
I have been looking at the Mclust plot page in: https://rdrr.io/cran/mclust/man/plot.Mclust.html and looking at the arguments of the function, I see there is a scope of adding other graphical parameters. Looking at the documentation of the plot function, there is a parameter called type = 'n' which might help to do what I want but when I write it, it produces the following error:
Error in plot.default(data[, 1], data[, 2], type = "n", xlab = xlab, ylab = ylab, :
formal argument "type" matched by multiple actual arguments
For reference, this is the code I used for the first plot:
library(mclust)
Data1_2 <- Mclust(Data, G=15)
summary(Data1_2, parameters = TRUE, classification = TRUE)
plot(Data1_2, what="classification")
The code I tried using for getting the graph below is:
Data1_4 <- Mclust(Data, G=8)
summary(Data1_4, parameters = TRUE, classification = TRUE)
plot(Data1_4, what="classification", type = "n")
Any help on this matter will be appreciated. Thanks!
If you look under the source code of plot.Mclust, it calls plot.Mclust.classification which in turn calls coordProj for the dot and ellipse plot. Inside this function, the size is controlled by the option CEX= and shape PCH=.
So for your purpose, do:
library(mclust)
clu = Mclust(iris[,1:4], G = 3, what="classification")
plot(clu,what="classification",CEX=0)
I am attempting to produce an NMDS plot in vegan, but really struggling with the code. I am trying to display the site points and species points differently, with the site points coloured according to treatment. Both lines work individually, but I cannot work out how to combine these two lines of code into one line to form one graph. I am using ordipointlabel to prevent overlap. These are the two lines of code I want to combine into one.
ordipointlabel(NMDS10, scaling=2, display="species", select=sel)
ordipointlabel(NMDS10,display="sites", col=c(rep("darkgreen",4),rep("blue4",4)),cex=0.75)
You can access directly to ordinpointlabel object and make it look like you wish. Please see the sample:
library(vegan)
data(dune)
NMDS10 <- metaMDS(dune[1:8, ])
pdf(file = NULL)
y <- ordipointlabel(NMDS10, display=c("sites", "species"))
dev.off()
# select sites & species
sel <- unlist(dimnames(dune[1:8, ]))[-(20:ncol(dune))]
# messing with ordipointlabel object
y$points <- y$points[rownames(y$points) %in% sel, ]
y$args$pcol[] = rep("red", length(y$args$pcol))
y$args$pcol[1:8] <- c(rep("darkgreen", 4), rep("blue4", 4))
y$par$cex <- 0.75
plot(y)
I´m recently trying to analyse my data and want to make the graphs a little nicer but I´m failing at this.
So I have a data set with 144 sites and 5 environmental variables. It´s basically about the substrate composition around an island and the fish abundance. On this island there is supposed to be a difference in the substrate composition between the north and the southside. Right now I am doing a pca and with the biplot function it works quite fine, but I would like to change the plot a bit.
I need one where the sites are just points and not numbered, arrows point to the different variable and the sites are colored according to their location (north or southside). So I tried everything i could find.
Most examples where with the dune data and suggested something like this:
library(vegan)
library(biplot)
data(dune)
mod <- rda(dune, scale = TRUE)
biplot(mod, scaling = 3, type = c("text", "points"))
So according to this I would just need to say text and points and R would label the variables and just make points for the sites. When i do this, however I get the Error:
Error in plot.default(x, type = "n", xlim = xlim, ylim = ylim, col = col[1L], :
formal argument "type" matched by multiple actual arguments
No idea how to get around this.
So next strategy I found, is to make a plot manually like this:
require("vegan")
data(dune, dune.env)
mod <- rda(dune, scale = TRUE)
scl <- 3 ## scaling == 3
colvec <- c("red2", "green4", "mediumblue")
plot(mod, type = "n", scaling = scl)
with(dune.env, points(mod, display = "sites", col = colvec[Use],
scaling = scl, pch = 21, bg = colvec[Use]))
text(mod,display="species", scaling = scl, cex = 0.8, col = "darkcyan")
with(dune.env, legend("bottomright", legend = levels(Use), bty = "n",
col = colvec, pch = 21, pt.bg = colvec))
This works fine so far as well, I get different colors and points, but now the arrows are missing. So I found that this should be corrected easy, if i just put "display="bp"" in the text line. But this doesn´t work either. Everytime I put "bp" R says:
Error in match.arg(display) :
argument "display" is missing, with no default
So I´m kind of desperate now. I looked through all the answers here and I don´t understand why display="bp" and type=c("text","points") is not working for me.
If anyone has an idea i would be super grateful.
https://www.dropbox.com/sh/y8xzq0bs6mus727/AADmasrXxUp6JTTHN5Gr9eufa?dl=0
This is the link to my dropbox folder. It contains my R-script and the csv files. The one named environmentalvariables_Kon1 also contains the data about north and southside.
So yeah...if anyone could help me. That would be awesome. I really don´t know what to do anymore.
Best regards,
Nancy
You can add arrows with arrows(). See the code for vegan:::biplot.rda to see how it works in the original function.
With your plot, add
g <- scores(mod, display = "species")
len <- 1
arrows(0, 0, len * g[, 1], len * g[, 2], length = 0.05, col = "darkcyan")
You might want to adjust the value of len to make the arrows longer
I would like to plot goups for my ordination using the function ordihull in vegan. However I have some sites with only one occurence. Using ordihull this sites do not appear in the plot. See the example below, when only one site has BF as management. What I would like to have is a BF label where the one remaining BF management site is located in the ordination plot.
library(vegan)
data(dune)
data(dune.env)
#remove all but one row with BF as management
dune <- dune[-c(2,11),]
dune.env <- dune.env[-c(2,11),]
mod <- cca(dune ~ Management, dune.env)
attach(dune.env)
plot(mod, type="n", scaling = 3)
pl <- ordihull(mod, Management, scaling = 3, label = TRUE)
orihull ignores groups with a single observation and thus doesn't populate the group centroids object with the centre of the convex hull. You could argue it should; I'll need to take this up with Jari and see if we can fix this.
To solve the problem, you have to add the location of the single observation in a secondary step using the text() method. [With the correct removal of all bar one of the BF observations -- -c(2,11)] the following does what you want:
plot(mod, type="n", scaling = 3)
with(dune.env, ordihull(mod, Management, scaling = 3, label = TRUE))
with(dune.env,
text(mod, labels = Management, select = Management == "BF",
scaling = 3, display = "sites"))
Giving
This is made trivial because you can specify select to choose to plot on the one observation with Management == "BF".
I want to have the box plotted with thicker lines. In boxplot function I simply put lwd=2, but in the lattice bwplot I can pull my hair out and haven't found a solution!
(with the box I mean the blue thing in the image above)
Sample code to work with:
require(lattice)
set.seed(123)
n <- 300
type <- sample(c("city", "river", "village"), n, replace = TRUE)
month <- sample(c("may", "june"), n, replace = TRUE)
x <- rnorm(n)
df <- data.frame(x, type, month)
bwplot(x ~ type|month, data = df, panel=function(...) {
panel.abline(h=0, col="green")
panel.bwplot(...)
})
As John Paul pointed out, the line widths are controlled by the the box.rectangle and box.umbrella components of lattice's graphical parameter list. (For your future reference, typing names(trellis.par.get()) is a fast way to scan the list of graphical attributes controlled by that list.)
Here's a slightly cleaner way to set those options for one or more particular figures:
thickBoxSettings <- list(box.rectangle=list(lwd=2), box.umbrella=list(lwd=2))
bwplot(x ~ type|month, data = df,
par.settings = thickBoxSettings,
panel = function(...) {
panel.abline(h=0, col="green")
panel.bwplot(...)
})
One thing you can do is get the trellis settings for the box, and change those. Try
rect.settings<-trellis.par.get("box.rectangle") #gets all rectangle settings
rect.settings$lwd<-4 #sets width to 4, you can choose what you like
trellis.par.set("box.rectangle",rect.settings)
Put these above your bwplot call and it should do it.
The box rectangle settings also has color, fill etc.
Edit to add if you get box.umbrella you can edit it to change what the lines above and below the box look like.
There is a further feature of lattice plots that needs mention. They are really objects, so methods exist for modifying their list representations;
myBW <- bwplot(x ~ type|month, data = df, panel=function(...) {
panel.abline(h=0, col="green")
panel.bwplot(...)
})
newBW <- update(myBW, par.settings=list(box.rectangle=list(lwd=4) ))
plot(newBW) # need to print or plot a grid object
You can also use trellis.focus and apply further updating function to overlay new data or text.