Error with GOAnnotations matrix and pRolocVis

[lmsimp]

This is almost certainly related to #76.

library('pRoloc')
library('pRolocdata')
library('pRolocGUI')
data("hyperLOPIT2015")
hyperLOPIT2015 <- markerMSnSet(hyperLOPIT2015)
params <- setAnnotationParams(inputs = c("Mus musculus", 
                                         "UniProt/Swissprot"))
cc <- addGoAnnotations(hyperLOPIT2015, params, 
                   namespace = "cellular_component")
pRolocVis(cc, fcol = "GOAnnotations")

Error in : fcol %in% fvarLabels(object) is not TRUE

With pRolocVis looks okay to start with... but then trying to zoom, then click an item in the table results in an error with regard to fcol

[lmsimp]

I now can not reproduce the above error.

But the issue I have is that if you pass a matrix of markers e.g. fcol = GOAnnotations then it appears as a long vector of 1's and 0's which is a bit ugly and also it's not at all informative. e.g.

[lmsimp]

So to fix this @lgatto I have changed the pRolocVis_pca code so that any fcol which is a matrix is converted to a vector using mrkMatToVec. I do this for all columns that are a matrix not just the one called by fcol as we also have to Table Selection tab where we can select other columns. So I want the same behaviour for all matrix of markers.

Is this okay with you @lgatto?

[lmsimp]

Fixed in 2c332d39430973616fa8716f47784b46da627db0

[lgatto]

Would it not be easier to do something like

fData(object) <- rbind(fData(object), fData(object)[, fcol])
fData(object)[, fcol] <- NULL

[lmsimp]

Dammit, yes it would be easier

[lmsimp]

I am now fixing a similar bug in pRolocVis_comp so will have a look at re-coding the above first...