PCA legend does not respect study.phenotype_order

[boyko-]

study.phenotype_order correctly sets the order of phenotypes on the violin plots, but not on the PCA legend. There are two ways to fix that:

1) PREFERRED: permute the colors on the PCA according to phenotype_order and order the phenotype labels in the PCA legend according to the same order. No need to change violin plots.

2) keep the colors and order of the PCA legend and permute the colors on the violin plot, while keeping their order consistent with study.phenotype_order

[olgabot]

Can you share a part of the datapackage you're using? It seems to be a bug in the coloring, not of the PCA legend.

[olgabot]

Example figure: https://github.com/YeoLab/flotilla/issues/111#issuecomment-57742680

[mlovci]

ok, now the pca legend is set correctly and the violin color order is right, but the violin label order is wrong, is that correct, @boyko- ?

[olgabot]

ping @boyko-