Improve plotSeries

[TuomasBorman]

plotSeries did not take into account that the data might include multiple systems, e.g,, bioreactors or patients. Moreover, as this function relates to miaTime package, the parameter naming was not harmonized.

I changed the parameter names without deprecating. I am not sure how widely this function is used.

Moreover, I added functionality that allows user to compare systems, here bioreactors. Each facet is unique taxon:

plotSeries(
    tse,
    time.col = "DAY_ORDER",
    assay.type = "counts",
    features = getTop(tse, 2),
    group = "Vessel",
    linetype.by = "Pre_Post_Challenge",
    scales = "free"
    )