plotArrow

[Kim-Anh Le Cao]

1. abline goes over the plot. I dont think we need abline, you could remove that (set to F for now)

2. issue with label option for multiblock? in multiblock setting show closer to the centroid? might need to rename that argument more explicitly - to be discussed at meeting.

data(nutrimouse) Y = unmap(nutrimouse$diet) data = list(gene = nutrimouse$gene, lipid = nutrimouse$lipid, Y = Y) design1 = matrix(c(0,1,1,1,0,1,1,1,0), ncol = 3, nrow = 3, byrow = TRUE) nutrimouse.sgcca <- wrapper.sgcca(blocks = data, design = design1, penalty = c(0.3, 0.5, 1), ncomp = c(2, 2, 3), scheme = "centroid", verbose = FALSE, bias = FALSE) plotArrow(nutrimouse.sgcca, group = nutrimouse$diet, add.legend =TRUE, main = 'my plot', ind.names = FALSE, label = TRUE)

3. for multiblock, centroid should be shown as a little star to stand out from the rest. for now it is not clear.

4. plot.arrows does not seem to work

5. do we need titlemain?? I would remove since you have main (I changed the name as subtitle).

3 files pushed on devel.graphique called 'plotArrow issue'

[Kim-Anh Le Cao]

plotArrow Code: function(object, comp = NULL, abline.line = FALSE, xlim = NULL, ylim = NULL, group = NULL, col, cex, pch, main = NULL, plot.arrows = TRUE, add.legend = FALSE, X.label = NULL, Y.label = NULL, label = FALSE) Docs: function(object, comp = NULL, ind.names = FALSE, abline.line = FALSE, xlim = NULL, ylim = NULL, group = NULL, col, cex, pch, main = NULL, plot.arrows = TRUE, add.legend = FALSE, subtitle = NULL, X.label = NULL, Y.label = NULL, label = FALSE) Argument names in docs not in code: ind.names subtitle Mismatches in argument names (first 3): Position: 3 Code: abline.line Docs: ind.names Position: 4 Code: xlim Docs: abline.line Position: 5 Code: ylim Docs: xlim

Also make sure Rd example works and running_scripts are updated Thanks!

[Kim-Anh Le Cao]

data(nutrimouse) X <- nutrimouse$lipid Y <- nutrimouse$gene nutri.res <- rcc(X, Y, ncomp = 3, lambda1 = 0.064, lambda2 = 0.008)

plotArrow(nutri.res)

Error in plotArrow(nutri.res) : 'ind.names' must be a character vector of length 40 or boolean or or 'on.points' or 'on.arrows' .

[Kim-Anh Le Cao]

data(nutrimouse) X <- nutrimouse$lipid Y <- nutrimouse$gene nutri.res <- rcc(X, Y, ncomp = 3, lambda1 = 0.064, lambda2 = 0.008)

plotArrow(nutri.res)

names indicate genotype

text appears 3 times for the same individual. Too much

plotArrow(nutri.res, group = nutrimouse$genotype, label = nutrimouse$genotype, cex = 0.8)

same remark as aaove

plotArrow(nutri.res, group = nutrimouse$genotype, label = TRUE, cex = 0.5)

the label 'on.arrows' is not explicit. Maybe chance to 'on centroid'? see remark on bitbucket on gcca too

plotArrow(nutri.res, group = nutrimouse$genotype, label = 'on.arrows', cex = 0.8)

text appears 2 times and should only appear at the start of the arrow (or the end, but one of those)

plotArrow(nutri.res, group = nutrimouse$genotype, label = 'on.points', cex = 0.8)

plotArrow(nutri.res, group = nutrimouse$genotype, add.legend = TRUE)

for sgcca

the 'on arrows' seems to mean on centroid??

[Kim-Anh Le Cao]

Similar to plotIndiv, issues with legend matching labels, key code in legend and lag in display for position.names. If the lag cannot be resolved we will go for whatever is easier (e.g. centroid or start per default). Pushed on bitbucket, see running script.

[Kim-Anh Le Cao]

done in V5.3 and v6