Plotting adonis (vegan) results

What Jari meant was if you use `betadisper()` on your data then it 
will
give you an object that has a `plot()` method which will give you 
something
of relevance to what `adonis()` and the whole PERMANOVA method is 
doing. It
plots the groups centroids and dispersions of the groups in principal
coordinates space. I don't have easy access to that journal at the 
minute,
but will look when I get back from this conference next week.

You can see how `betadisper` and its `plot` method works in the mean 
time
if you want to customise how things are plotted.

Gavin

On 9 August 2013 06:54, <Jonas.Persson at niva.no> wrote:

Hi all

I'd like to plot my results from adonis (vegan). Internet searches 
found
me an older post here in which Jari Oksanen wrote: "adonis() does not 
have
plot method, but  you can use betadisper for plots." But I'm afraid I
don't understand how to do it this way.

How can I a) make a plot of adonis results? b) manipulate the layout 
of
adonis/betadispers figures to my liking?
My main inspiration for both adonis and betadispers results plotting 
is
Friberg et al (2013) Hydrol. Process. 27, 734?740, so I'd like to be 
able
to produce something similar.

Cheers,
Jonas

Just one point Vit, re "...or choose another ordination technique." If 
by
that you meant you could use PCA or CA or NMDS etc, then I don't think 
that
will be useful. We use PCoA because the inputs to adonis(), 
betadisper, etc
are dissimilarity matrices and the aim is to show those 
dissimilarities
(and the group centroids/dispersions) as best as possible whilst 
preserving
the direct link to the distance values (ie why we don't use NMDS). I 
guess
you could use PCA for this if you have Euclidean distances, CA if you 
want
Chi-square etc, but not NMDS as it works on ranks so you'd get an odd
representation of what adonis() or betadisper() do.

As for the rest, you seem to have that right, though the cmdscale() 
call
might take a little bit more effort if you want to handle negative
Eigenvalues that arise with some dissimilarity metrics.


On 10 August 2013 06:33, V?t Syrov?tka <syrovat at sci.muni.cz> wrote:

Dear Jonas,
I've just had a look into the paper (Friberg et al (2013)), but there 
is
no information on what kind of ordination they used (at least it is 
very
well hidden). Hard to believe, maybe I am wrong, but can't find 
anything
about that. And they used different ordination techniques to 
visualise the
groups with regard to the results of 'adonis()' and 'betadisper()' -
compare Fig.1 and Fig. 2. Maybe that brought the confusion.

The thing is that 'adonis()' tells you, whether the groups 
consistently
differ in their community composition, and then it's up to you to 
chose an
ordination technique to visualize the groups. Probably that would be 
an
ordination that approximates the same distances used in 'adonis()' 
(or
'betadisper()'). The plot method of 'betadisper()' uses Principal
Coordinate Analysis (PCoA), which you can use to visualize the 
results of
'adonis()' as well (as Gavin and Jari pointed out) or do it by your 
own or
choose another ordination technique.

A small example with PCoA:

## taken from ?betadisper:
library(vegan)
data(varespec)

# create the dist object
dis <- vegdist(varespec)

# create grouping variable; First 16 sites grazed, remaining 8 sites
ungrazed
groups <- factor(c(rep(1,16), rep(2,8)), labels = 
c("grazed","ungrazed"))

# Calculate multivariate dispersions
mod <- betadisper(dis, groups)

# Plot PCoA ordination with differentiated groups = visualize the
dispersions of groups in 2D ordination space
plot(mod)

## now create the same plot on my own (though with different graphic
parameters)
# calculate the PCoA ordination sites' scores
pcoa<- cmdscale(dis)
# plot them with different symbols for groups
plot(pcoa, asp=1)
# and add spiders and hulls
ordispider(pcoa, groups)
ordihull(pcoa, groups)

If I am wrong in any point, will be glad if someone corrects me.
Cheers,
Vit


Dne 2013-08-09 19:25, Gavin Simpson napsal:

 What Jari meant was if you use `betadisper()` on your data then it 
will

give you an object that has a `plot()` method which will give you
something
of relevance to what `adonis()` and the whole PERMANOVA method is 
doing.
It
plots the groups centroids and dispersions of the groups in 
principal
coordinates space. I don't have easy access to that journal at the 
minute,
but will look when I get back from this conference next week.

You can see how `betadisper` and its `plot` method works in the mean 
time
if you want to customise how things are plotted.

Gavin

On 9 August 2013 06:54, <Jonas.Persson at niva.no> wrote:

 Hi all

I'd like to plot my results from adonis (vegan). Internet searches 
found
me an older post here in which Jari Oksanen wrote: "adonis() does 
not
have
plot method, but  you can use betadisper for plots." But I'm afraid 
I
don't understand how to do it this way.

How can I a) make a plot of adonis results? b) manipulate the 
layout of
adonis/betadispers figures to my liking?
My main inspiration for both adonis and betadispers results 
plotting is
Friberg et al (2013) Hydrol. Process. 27, 734?740, so I'd like to 
be able
to produce something similar.

Cheers,
Jonas