plotConv: Graphical representation of search.conv results
In RRphylo: Phylogenetic Ridge Regression Methods for Comparative Studies
plotConv R Documentation
Graphical representation of search.conv results
Description
This function generates customized functions to produce plots out of
search.conv results.
Usage
plotConv(SC,y,variable,RR=NULL,state=NULL,aceV=NULL)
Arguments
SC
an object produced by search.conv.
y
the multivariate phenotype used to perform search.conv.
variable
the index of result to plot. If convergence between clades is
inspected, this is the position within the SC$'average distance from
group centroids' vector of the clade pair to be plotted. In the case of
convergence between states, this is the number of the line of
SC$state.res where results for the state pair are returned.
RR
the object produced by RRphylo used to perform
search.conv. This is not indicated if convergence between states is
tested.
state
the named vector of tip states used to perform search.conv.
This is not indicated if convergence between clades is tested.
aceV
phenotypic values at internal nodes to be provided if used to
perform search.conv.
Value
If convergence between clades was tested, plotConv returns a
list of four functions:
$plotHistTips shows the mean Euclidean distance
computed between phenotypic vectors of all the tips belonging to the
converging clades as compared to the distribution of distances between all
possible pair of tips across the rest of the tree. The usage is:
...$plotHistTips(hist.args=NULL,line.args=NULL), where
hist.args is a list of further arguments passed to the function
hist, and line.args is a list of further arguments passed to
the function lines.
$plotHistAces shows the Euclidean distance computed
between phenotypic vectors of the MRCAs of the converging clades as compared
to the distribution of distances between all possible pairs of nodes across
the rest of the tree. The usage is identical to $plotHistTips.
$plotPChull generates a PC1/PC2 plot obtained by
performing a PCA of the species phenotypes. Convergent clades are indicated
by colored convex hulls. Large dots represent the mean phenotypes per clade
(i.e. their group centroids) and asterisks (customizable) represent the
ancestral phenotypes of the individual clades. The usage is:
...$plotPChull(plot.args=NULL,chull.args=NULL,means.args=NULL,
ace.args=NULL,legend.args=list(),where plot.args is a list of
further arguments passed to the function plot, chull.args is a
list of further arguments passed to the function polygon,
means.args and ace.args are lists of further argument passed
to the function points to customize the dots representing the
centroids and the ancestral phenotypes respectively, and legend.args
is a list of additional arguments passed to the function legend (if
= NULL the legend is not plotted).
$plotTraitgram produces a modified traitgram plot (see
package picante) highlighting the branches of the clades found to
converge. The usage is:
plotTraitgram(colTree=NULL,colNodes=NULL,...), where colTree
is the color to represent the traitgram lines not pertaining the converging
clades, colNodes is the color (or the vector of colors) to represent
the traitgram lines pertaining the converging clades, and ... are
further arguments passed to the function plot to plot lines.
If convergence between states was tested, plotConv returns a
list of two functions:
$plotPChull generates a PC1/PC2 plot obtained by
performing a PCA of the species phenotypes, with colored convex hulls
enclosing species belonging to different states. The usage is:
...$plotPChull(plot.args=NULL,chull.args=NULL,points.args=NULL,
legend.args=list(), where plot.args is a list of further
arguments passed to the function plot, chull.args is a list of
further arguments passed to the function polygon, points.args
is a list of further argument passed to the function points, and
legend.args is a list of additional arguments passed to the function
legend (if = NULL the legend is not plotted).
$plotPolar produces a polar plot of the mean angle
within/between state/s as compared to the 95
angles. The usage is:
...$plotPolar(polar.args=NULL,polygon.args=NULL,line.args=NULL),
where polar.args is a list of further arguments passed to the
function polar.plot to set the plot basics (i.e.
radial.lim, start, and so on), polygon.args is a list
of further arguments passed to the function polar.plot under the
condition rp.type="p" (see plotrix::polar.plot for details) to
set the angles distribution graphics, and line.args is a list of
further arguments passed to the function polar.plot under the
condition rp.type="r" to set the mean angle graphics.
Author(s)
Silvia Castiglione
References
Castiglione, S., Serio, C., Tamagnini, D., Melchionna, M.,
Mondanaro, A., Di Febbraro, M., Profico, A., Piras, P.,Barattolo, F., &
Raia, P. (2019). A new, fast method to search for morphological convergence
with shape data. PLoS ONE, 14, e0226949.
https://doi.org/10.1371/journal.pone.0226949
See Also
Examples
## Not run:
data("DataFelids")
DataFelids$PCscoresfel->PCscoresfel
DataFelids$treefel->treefel
DataFelids$statefel->statefel->state2
state2[sample(which(statefel=="nostate"),20)]<-"st2"
cc<- 2/parallel::detectCores()
RRphylo(treefel,PCscoresfel,clus=cc)->RRfel
search.conv(RR=RRfel, y=PCscoresfel, min.dim=5, min.dist="node9",clus=cc)->sc.clade
plotConv(sc.clade,PCscoresfel,variable=2,RR=RRfel)->pc.clade
pc.clade$plotHistTips(hist.args = list(col="gray80",yaxt="n",cex.axis=0.8,cex.main=1.5),
line.args = list(lwd=3,lty=4,col="purple"))
pc.clade$plotHistAces(hist.args = list(col="gray80",cex.axis=0.8,cex.main=1.5),
line.args = list(lwd=3,lty=4,col="gold"))
pc.clade$plotPChull(chull.args = list(border=c("cyan","magenta"),lty=1),
means.args = list(pch=c(23,22),cex=3,bg=c("cyan2","magenta2")),
ace.args=list(pch=9),legend.args = NULL)
pc.clade$plotTraitgram(colTree = "gray70",colNodes = c("cyan","magenta"))
search.conv(tree=treefel, y=PCscoresfel, state=statefel,declust=TRUE,clus=cc)->sc.state
plotConv(sc.state,PCscoresfel,variable=1,state=statefel)->pc.state
pc.state$plotPChull(chull.args = list(border=c("gray70","blue"),lty=1),
points.args = list(pch=c(23,22),bg="gray"),
legend.args = list(pch=c(23,22),x="top"))
pc.state$plotPolar(polar.args = list(clockwise=TRUE,start=0,rad.col="black",grid.col="black"),
polygon.args = list(line.col="green",poly.col=NA,lwd=2),
line.args = list(line.col="deeppink",lty=2,lwd=3))
## End(Not run)
RRphylo documentation built on Aug. 8, 2025, 6:37 p.m.
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| plotConv | R Documentation |
Graphical representation of search.conv results
Description
This function generates customized functions to produce plots out of
search.conv results.
Usage
plotConv(SC,y,variable,RR=NULL,state=NULL,aceV=NULL)
Arguments
SC |
an object produced by |
y |
the multivariate phenotype used to perform |
variable |
the index of result to plot. If convergence between clades is
inspected, this is the position within the |
RR |
the object produced by |
state |
the named vector of tip states used to perform |
aceV |
phenotypic values at internal nodes to be provided if used to
perform |
Value
If convergence between clades was tested, plotConv returns a
list of four functions:
$plotHistTips shows the mean Euclidean distance
computed between phenotypic vectors of all the tips belonging to the
converging clades as compared to the distribution of distances between all
possible pair of tips across the rest of the tree. The usage is:
...$plotHistTips(hist.args=NULL,line.args=NULL), where
hist.args is a list of further arguments passed to the function
hist, and line.args is a list of further arguments passed to
the function lines.
$plotHistAces shows the Euclidean distance computed
between phenotypic vectors of the MRCAs of the converging clades as compared
to the distribution of distances between all possible pairs of nodes across
the rest of the tree. The usage is identical to $plotHistTips.
$plotPChull generates a PC1/PC2 plot obtained by
performing a PCA of the species phenotypes. Convergent clades are indicated
by colored convex hulls. Large dots represent the mean phenotypes per clade
(i.e. their group centroids) and asterisks (customizable) represent the
ancestral phenotypes of the individual clades. The usage is:
...$plotPChull(plot.args=NULL,chull.args=NULL,means.args=NULL,
ace.args=NULL,legend.args=list(),where plot.args is a list of
further arguments passed to the function plot, chull.args is a
list of further arguments passed to the function polygon,
means.args and ace.args are lists of further argument passed
to the function points to customize the dots representing the
centroids and the ancestral phenotypes respectively, and legend.args
is a list of additional arguments passed to the function legend (if
= NULL the legend is not plotted).
$plotTraitgram produces a modified traitgram plot (see
package picante) highlighting the branches of the clades found to
converge. The usage is:
plotTraitgram(colTree=NULL,colNodes=NULL,...), where colTree
is the color to represent the traitgram lines not pertaining the converging
clades, colNodes is the color (or the vector of colors) to represent
the traitgram lines pertaining the converging clades, and ... are
further arguments passed to the function plot to plot lines.
If convergence between states was tested, plotConv returns a
list of two functions:
$plotPChull generates a PC1/PC2 plot obtained by
performing a PCA of the species phenotypes, with colored convex hulls
enclosing species belonging to different states. The usage is:
...$plotPChull(plot.args=NULL,chull.args=NULL,points.args=NULL,
legend.args=list(), where plot.args is a list of further
arguments passed to the function plot, chull.args is a list of
further arguments passed to the function polygon, points.args
is a list of further argument passed to the function points, and
legend.args is a list of additional arguments passed to the function
legend (if = NULL the legend is not plotted).
$plotPolar produces a polar plot of the mean angle
within/between state/s as compared to the 95
angles. The usage is:
...$plotPolar(polar.args=NULL,polygon.args=NULL,line.args=NULL),
where polar.args is a list of further arguments passed to the
function polar.plot to set the plot basics (i.e.
radial.lim, start, and so on), polygon.args is a list
of further arguments passed to the function polar.plot under the
condition rp.type="p" (see plotrix::polar.plot for details) to
set the angles distribution graphics, and line.args is a list of
further arguments passed to the function polar.plot under the
condition rp.type="r" to set the mean angle graphics.
Author(s)
Silvia Castiglione
References
Castiglione, S., Serio, C., Tamagnini, D., Melchionna, M., Mondanaro, A., Di Febbraro, M., Profico, A., Piras, P.,Barattolo, F., & Raia, P. (2019). A new, fast method to search for morphological convergence with shape data. PLoS ONE, 14, e0226949. https://doi.org/10.1371/journal.pone.0226949
See Also
Examples
## Not run:
data("DataFelids")
DataFelids$PCscoresfel->PCscoresfel
DataFelids$treefel->treefel
DataFelids$statefel->statefel->state2
state2[sample(which(statefel=="nostate"),20)]<-"st2"
cc<- 2/parallel::detectCores()
RRphylo(treefel,PCscoresfel,clus=cc)->RRfel
search.conv(RR=RRfel, y=PCscoresfel, min.dim=5, min.dist="node9",clus=cc)->sc.clade
plotConv(sc.clade,PCscoresfel,variable=2,RR=RRfel)->pc.clade
pc.clade$plotHistTips(hist.args = list(col="gray80",yaxt="n",cex.axis=0.8,cex.main=1.5),
line.args = list(lwd=3,lty=4,col="purple"))
pc.clade$plotHistAces(hist.args = list(col="gray80",cex.axis=0.8,cex.main=1.5),
line.args = list(lwd=3,lty=4,col="gold"))
pc.clade$plotPChull(chull.args = list(border=c("cyan","magenta"),lty=1),
means.args = list(pch=c(23,22),cex=3,bg=c("cyan2","magenta2")),
ace.args=list(pch=9),legend.args = NULL)
pc.clade$plotTraitgram(colTree = "gray70",colNodes = c("cyan","magenta"))
search.conv(tree=treefel, y=PCscoresfel, state=statefel,declust=TRUE,clus=cc)->sc.state
plotConv(sc.state,PCscoresfel,variable=1,state=statefel)->pc.state
pc.state$plotPChull(chull.args = list(border=c("gray70","blue"),lty=1),
points.args = list(pch=c(23,22),bg="gray"),
legend.args = list(pch=c(23,22),x="top"))
pc.state$plotPolar(polar.args = list(clockwise=TRUE,start=0,rad.col="black",grid.col="black"),
polygon.args = list(line.col="green",poly.col=NA,lwd=2),
line.args = list(line.col="deeppink",lty=2,lwd=3))
## End(Not run)
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