Example for the plotScoreLandscape in the vignette

[MomenehForoutan]

Hey @Rachael-rq , One of the examples for this function is not quite right; I know it is just an example, but we should not swap the up and down sets of the TGFb-EMT signature to generate a new score data frame; it may confuse people. Here is what you have written:

#  For illustration of the function, we generate scoredf1 using 
# upSet = tgfb_gs_dn, downSet = tgfb_gs_up,
# generate scoredf2 using upSet = tgfb_gs_dn, downSet = tgfb_gs_up
scoredf1 <- simpleScore(rankData, upSet = tgfb_gs_up, downSet = tgfb_gs_dn)
scoredf2 <- simpleScore(rankData, upSet = tgfb_gs_dn, downSet = tgfb_gs_up)

plotScoreLandscape(scoredf1, scoredf2, scorenames = c('tgfb_gs',
                                                      'tgfb_gs_reverse'))

How about if we remove the above example and only go with the CCLE and TCGA examples that you have also already included? Which is like:

data("scoredf_ccle_epi")
data("scoredf_ccle_mes")
plotScoreLandscape(scoredf_ccle_epi, scoredf_ccle_mes, 
                   scorenames = c('ccle-EPI','ccle-MES'),hexMin = 10)

So that we only need to mention that for the epithelial and mesenchymal signatures without the down set, we need to set downSet = NULL in the simpleScore function. What do you thinks @bhuvad ? Cheers, Sepideh