dapc graphics | R Documentation |
These functions provide graphic outputs for Discriminant Analysis of
Principal Components (DAPC, Jombart et al. 2010). See ?dapc
for
details about this method. DAPC graphics are detailed in the DAPC tutorial
accessible using vignette("adegenet-dapc")
.
These functions all require an object of class dapc
(the ".dapc" can be ommitted when calling the functions):
- scatter.dapc
: produces scatterplots of principal components (or
'discriminant functions'), with a screeplot of eigenvalues as inset.
- assignplot
: plot showing the probabilities of assignment of
individuals to the different clusters.
## S3 method for class 'dapc' scatter(x, xax=1, yax=2, grp=x$grp, col=seasun(length(levels(grp))), pch=20, bg="white", solid=.7, scree.da=TRUE, scree.pca=FALSE, posi.da="bottomright", posi.pca="bottomleft", bg.inset="white", ratio.da=.25, ratio.pca=.25, inset.da=0.02, inset.pca=0.02, inset.solid=.5, onedim.filled=TRUE, mstree=FALSE, lwd=1, lty=1, segcol="black", legend=FALSE, posi.leg="topright", cleg=1, txt.leg=levels(grp), cstar = 1, cellipse = 1.5, axesell = FALSE, label = levels(grp), clabel = 1, xlim = NULL, ylim = NULL, grid = FALSE, addaxes = TRUE, origin = c(0,0), include.origin = TRUE, sub = "", csub = 1, possub = "bottomleft", cgrid = 1, pixmap = NULL, contour = NULL, area = NULL, label.inds = NULL, ...) assignplot(x, only.grp=NULL, subset=NULL, new.pred=NULL, cex.lab=.75,pch=3)
x |
a |
xax,yax |
|
grp |
a factor defining group membership for the individuals. The scatterplot is optimal only for the default group, i.e. the one used in the DAPC analysis. |
col |
a suitable color to be used for groups. The specified vector should match the number of groups, not the number of individuals. |
pch |
a |
bg |
the color used for the background of the scatterplot. |
solid |
a value between 0 and 1 indicating the alpha level for the colors of the plot; 0=full transparency, 1=solid colours. |
scree.da |
a logical indicating whether a screeplot of Discriminant Analysis eigenvalues should be displayed in inset (TRUE) or not (FALSE). |
scree.pca |
a logical indicating whether a screeplot of Principal Component Analysis eigenvalues should be displayed in inset (TRUE) or not (FALSE); retained axes are displayed in black. |
posi.da |
the position of the inset of DA eigenvalues; can match any combination of "top/bottom" and "left/right". |
posi.pca |
the position of the inset of PCA eigenvalues; can match any combination of "top/bottom" and "left/right". |
bg.inset |
the color to be used as background for the inset plots. |
ratio.da |
the size of the inset of DA eigenvalues as a proportion of the current plotting region. |
ratio.pca |
the size of the inset of PCA eigenvalues as a proportion of the current plotting region. |
inset.da |
a vector with two numeric values (recycled if needed) indicating
the inset to be used for the screeplot of DA eigenvalues as a proportion of the
current plotting region; see |
inset.pca |
a vector with two numeric values (recycled if needed) indicating
the inset to be used for the screeplot of PCA eigenvalues as a proportion of the
current plotting region; see |
inset.solid |
a value between 0 and 1 indicating the alpha level for the colors of the inset plots; 0=full transparency, 1=solid colours. |
onedim.filled |
a logical indicating whether curves should be filled when plotting a single discriminant function (TRUE), or not (FALSE). |
mstree |
a logical indicating whether a minimum spanning tree linking the groups and based on the squared distances between the groups inside the entire space should added to the plot (TRUE), or not (FALSE). |
lwd,lty,segcol |
the line width, line type, and segment colour to be used for the minimum spanning tree. |
legend |
a logical indicating whether a legend for group colours should added to the plot (TRUE), or not (FALSE). |
posi.leg |
the position of the legend for group colours; can match any
combination of "top/bottom" and "left/right", or a set of x/y coordinates stored
as a list ( |
cleg |
a size factor used for the legend. |
cstar,cellipse,axesell,label,clabel,xlim,ylim,grid,addaxes,origin,include.origin,sub,csub,possub,cgrid,pixmap,contour,area |
arguments
passed to |
only.grp |
a |
subset |
|
new.pred |
an optional list, as returned by the |
cex.lab |
a |
txt.leg |
a character vector indicating the text to be used in
the legend; if not provided, group names stored in |
label.inds |
Named list of arguments passed to the
|
... |
further arguments to be passed to other functions. For
|
See the documentation of dapc
for more information about the method.
All functions return the matched call.
Thibaut Jombart t.jombart@imperial.ac.uk
Jombart T, Devillard S and Balloux F (2010) Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genetics11:94. doi:10.1186/1471-2156-11-94
- dapc
: implements the DAPC.
- find.clusters
: to identify clusters without prior.
- dapcIllus
: a set of simulated data illustrating the DAPC
- eHGDP
, H3N2
: empirical datasets illustrating
DAPC
## Not run: data(H3N2) dapc1 <- dapc(H3N2, pop=H3N2$other$epid, n.pca=30,n.da=6) ## defautl plot ## scatter(dapc1) ## label individuals at the periphery # air = 2 is a measure of how much space each label needs # pch = NA suppresses plotting of points scatter(dapc1, label.inds = list(air = 2, pch = NA)) ## showing different scatter options ## ## remove internal segments and ellipses, different pch, add MStree scatter(dapc1, pch=18:23, cstar=0, mstree=TRUE, lwd=2, lty=2, posi.da="topleft") ## only ellipse, custom labels, use insets scatter(dapc1, cell=2, pch="", cstar=0, posi.pca="topleft", posi.da="topleft", scree.pca=TRUE, inset.pca=c(.01,.3), label=paste("year\n",2001:2006), axesel=FALSE, col=terrain.colors(10)) ## without ellipses, use legend for groups scatter(dapc1, cell=0, cstar=0, scree.da=FALSE, clab=0, cex=3, solid=.4, bg="white", leg=TRUE, posi.leg="topleft") ## only one axis scatter(dapc1,1,1,scree.da=FALSE, legend=TRUE, solid=.4,bg="white") ## example using genlight objects ## ## simulate data x <- glSim(50,4e3-50, 50, ploidy=2) x plot(x) ## perform DAPC dapc2 <- dapc(x, n.pca=10, n.da=1) dapc2 ## plot results scatter(dapc2, scree.da=FALSE, leg=TRUE, txt.leg=paste("group", c('A','B')), col=c("red","blue")) ## SNP contributions loadingplot(dapc2$var.contr) loadingplot(tail(dapc2$var.contr, 100), main="Loading plot - last 100 SNPs") ## assignplot / compoplot ## assignplot(dapc1, only.grp=2006) data(microbov) dapc3 <- dapc(microbov, n.pca=20, n.da=15) compoplot(dapc3, lab="") ## End(Not run)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.