| draw.octopucs {octopucs} | R Documentation |
Draw the Generalized Clustering Hypothesis
Description
Draws the resulting generalized cluster with tips facing either down, left or right.
Usage
draw.octopucs(M2, cex=1, lab.pos=0.09, n=NULL,
distance=NULL, method=NULL, prop=NULL, Name=NULL, ylim=NULL, xlim=NULL,
verbose=NULL, orientation=NULL, support=NULL, sep.lab=NULL, disp = NULL)
Arguments
M2 |
A lis object generated by glzcluster or glzcluster2 |
cex |
Size of text in the figure |
lab.pos |
This argument modifies the position of the labels relative to the tips of the dendrogram (sites/conditions). |
n |
This is defined in the glzcluster or glzcluster2 functions. Number of bootstrap samples performed. |
distance |
Distance method used (default="bray"). This is defined in the glzcluster or glzcluster2 functions. Options include those of the function "vegdist" ("vegan"): "manhattan", "euclidean", "canberra", "bray", "kulczynski", "gower", "morisita", "horn", "mountford", "jaccard", "raup", "binomial", "chao", "altGower", "cao" and "mahalanobis", as well as those referred in Koleff et al. (2003), available either by name or number: 1 or "w", 2 or "-1", 3 or "c", 4 or "wb", 5 or "r", 6 or "I", 7 or "e", 8 or "t", 9 or "me", 10 or "j", 11 or "sor", 12 or "m", 13 or "-2", 14 or "co", 15 or "cc", 16 or "g", 17 or "-3", 18 or "1", 19 or "", 20 or "hk", 21 or "rlb", 22 or "sim", 23 or "gl", 24 or "z". For open distance metrics (not restricted to zero-one ranges), the axis is re-scaled to cover a zero-one range. If so, the axis will be labeled a "Similarity (rescaled)"; if no re-scaling is necessary, the label will appear as "Similarity". |
method |
This is defined in the glzcluster or glzcluster2 functions. Agglomerative procedure for hierarchical clustering, including: "average" (=UPGMA), "ward.D", "ward.D2", "single", "complete", "mcquitty" (=WPGMA), "median" (=WPGMC) or "centroid" (=UPGMC). |
prop |
This is defined in the glzcluster or glzcluster2 functions. Proportion of information used in the bootstrapping procedures. When matrices contain more than 18 columns, it refers to: (i) the proportion of columns used in every run to produce a new grouping array when "resample=TRUE" and (ii) the amount of cells in the body of the matrix (1–prop; e.g., 1–0.8=0.2) that will be replaced with column averages when "resample=FALSE". When matrices contain less than 18 columns, the procedure with "resample=FALSE" will be forced. In such scenario, "prop" corresponds to the amount of cells in the body of the matrix (1–prop; e.g., 1–0.8=0.2) that will be replaced in the bootstrapping procedures. |
Name |
Name of the database run on octopucs |
xlim |
Limits of the x-axis |
ylim |
Limits of the y-axis |
verbose |
TRUE = display all relevant setup values used in the analysis. FALSE = display only the dendrogram with marked significantly grouped clusters. |
orientation |
Any of d, l, or r denoting the orientation of the tips (down, left, and right, respectively) |
support |
A matrix object generated by the function glzcs |
sep.lab |
This argument modifies the position of supporting values from the nodes and lines and the dendrogram. |
disp |
What to display in relation to supporting values for the groups and subgroups. By default is set to "sig" and then support values are shown only in those groups statistically supported. |
Value
This function draws and if requested, populate with support metrics the consesnsus hypothesis of clustering
Author(s)
Roger Guevara (roger.guevara@inecol.mx) & Ian MacGregor-Fors (ian.macgregor@helsinki.fi)
References
Koleff, P., Gaston, K.J., Lennon, J. J. 2003. Measuring beta diversity for presence–absence data. Journal of Animal Ecology 71:367. https://doi.org/10.1046/j.1365-2656.2003.00710.x
Examples
data(dune)
rownames(dune)<- paste("S",1:20, sep="")
OCT <- glzcluster(dune, n=100)
GRP <- IDscluster(OCT)
SUP <- glzcs(GRP, OCT)
draw.octopucs(OCT, support=SUP)