plotIndiv

[Kim-Anh Le Cao]

I renamed plot.cent as plot.centroid

1. should plot.star only applied when argument group is provided? OK
2. should plot.centroid only applied when argument group is provided? OK
3. add examples with plot.star and plot.centroid in running test OK, partly
4. update help file OK
5. Indicate the centroid as a thick black 'star' otherwise it does not show on its own

Start from the 3 files named 'issue plotIndiv in devel.graphique'

[Kim-Anh Le Cao]

plotIndiv

Code: function(object, comp = NULL, rep.space = NULL, blocks = NULL, ind.names = TRUE, group, col.per.group, style = "lattice", plot.ellipse = TRUE, ellipse.level = 0.95, plot.centroid = TRUE, plot.star = FALSE, main = NULL, add.legend = FALSE, X.label = NULL, Y.label = NULL, Z.label = NULL, abline.line = FALSE, xlim = NULL, ylim = NULL, col, cex, pch, alpha = 0.2, axes.box = "box")

Docs: function(object, comp = NULL, rep.space = NULL, blocks = NULL, ind.names = TRUE, group, col.per.group, style = "ggplot2", plot.ellipse = FALSE, ellipse.level = 0.95, plot.centroid = FALSE, plot.star = FALSE, main = NULL, add.legend = FALSE, X.label = NULL, Y.label = NULL, Z.label = NULL, abline.line = FALSE, xlim = NULL, ylim = NULL, col, cex, pch, alpha = 0.2, axes.box = "box") Mismatches in argument default values: Name: 'style' Code: "lattice" Docs: "ggplot2" Name: 'plot.ellipse' Code: TRUE Docs: FALSE Name: 'plot.centroid' Code: TRUE Docs: FALSE

[Kim-Anh Le Cao]

plot of individuals for objects of class 'plsda' or 'splsda'

----------------------------------------------------

data(breast.tumors) X <- breast.tumors$gene.exp Y <- breast.tumors$sample$treatment

splsda.breast <- splsda(X, Y,keepX=c(10,10),ncomp=2)

only shows 1 star when you should see 2 (by default from group)

plotIndiv(splsda.breast, plot.centroid = T)

also, is there a way to color the stars according to the group (internal) or col.group?

[Kim-Anh Le Cao]

Hello, I havent tested your push from last night (conflicts) but I have further issues.

Before I was working with the updated plotIndiv script (see attached) and it was giving the right figure - except! that the legend key was wrong.

Now, with the non-pushed mixOmics devel.graphique I get this (see attached) * title block X still there for a sPLSDA * legend lty does not work well. Could we put pch = 16 by default please? * legend key is right

[Kim-Anh Le Cao]

Ok, forget about the above I think I had the wrong version.

Testing the plotIndiv you pushed, we have issues with the legend and labelling. See attached. The running script is on bitbucket (noted #FB). Seems to be an issue when there are more than 2 classes. Test thoroughly please.

[Kim-Anh Le Cao]

V5.3