immediate graphical improvements

[Kim-Anh Le Cao]

• plotVar: add plot= TRUE argument ok

FB: could you check that by default comp.select = comp and that by default comp = c(1,2).

Update .Rd file too

• plotIndiv

1. if(object == sgccda) then do not plot the Y block

need to link with Devel sgccda function from Florian.

2. by default, seems that plotIndiv.pls only show the X rep space, while the sgccda shows all res.space. I think by default pls and gcca should show all spaces (i.e. amend spls / spls so that it shows X-rep and Y-rep, 2 plots, by default). same for RCC. OK

3. • the plotIndiv by default shows as title: Block:X in PCA. Could we remove that title in all single omics methods? (PCA, IPCA, SPCA, sIPCA, PLSDA, sPLSDA)

Explained variance for PCA (only): 'PC1: 11.36 %', SPACE ISSUE left

4. added 3D, 3D ellipses and alpha (btw 0 and 1) OK

• cim: send example where similarity > 1? OK .Rd file to notify users that we are defining a similarity (KA) users bugs to fix, 2 issues reported

• network: added argument save. OK

• plotPerf: remove playwith for this patch OK

• barplots of eigenvalues for PCA OK

• plotArrow: put x and y axes as a normal plot.

[fbartolo]

cim example

data(nutrimouse) X <- nutrimouse$gene Y <- nutrimouse$lipid[,1:5] res.pls1 <- pls(X, Y, ncomp = 10, mode = "canonical") cim(res.pls1)

[fbartolo]

ok all

[fbartolo]

ok all

[fbartolo]

ok all

[Kim-Anh Le Cao]

V5.3 and V6