immediate graphical improvements

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Issue #41 resolved
Kim-Anh Le Cao repo owner created an issue
  • 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.

  1. 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

    • 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

  1. 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.

Comments (18)

  1. 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)

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