On 08/08/2017 03:59 AM, Angerer, Philipp wrote:
Hi Aaron,
I guess this would be a question for the SummarizedExperiment developers,
though personally, I never liked ExpressionSet's inclination to slap names on
everything.
Too bad we’re bound to SummarizedExperiment’s “rows” and “cols”. Since they
always refer to features and samples, respectively: Why not name them that?
There’s already too many APIs in too many programming languages that
confusingly have one or the other convention – if whe know which is which, why
not name them after that knowledge?
BQ_BEGIN
It probably wouldn't be a good idea to store distances as expression matrices.
However, if there is a need for it, we can add a new slot for distance
matrices. I think SC3 has a similar requirement, so perhaps this would be more
generally useful than I first thought. You can post an issue on the github
repository to remind Davide or me to do it.
BQ_END
Distance matrices (cell×cell) can’t only come from cell×gene matrices. You can
e.g. use dynamic time warping to create them from cell×gene×time arrays.
BQ_BEGIN
Finally, I'm not sure what advantages those ergonomics provide. Indeed, if
every package defines its own plot() S4 method for SingleCellExperiment, they
will clobber each other in the dispatch table, resulting in some interesting
results dependent on package loading order. If you have destiny-specific data
and methods, best to keep them separate rather than stuffing them into the SCE
object.
BQ_END
I wrote that I could e.g. create a plot_dm method, which plots a diffusion map
stored in a SCE.
Also I didn’t mean the plot method with ergonomics. I meant fortify , names , $
, and [[ . Those would be very useful, as you could just do things like the
following, and have autocompletion:
sce$Predicate1 <- sce$SampleMeta1 > 40 # `$` accesses counts (by gene) and
rowData. `$<-` sets rowData
qplot(Gene1, Gene2, colour = Predicate1, data = sce) # fortify creates a
data.frame containing cbind(t(counts), rowData)
FWIW, SummarizedExperiment (hence SingleCellExperimet) uses $ (and $<-;
also [[ and [[<-) to access (with auto-completion) colData. And it
wouldn't be a good idea to have $ access one element (counts) and $<-
modify another (rowData), or to mix what $ and [[ access.
Martin
Just as you can do now with DiffusionMap objects.
Also I’m not sure if i got rowData and the “t” right in the above code ;) I
meant cbind(counts as cell×gene, sampleMeta as cell×n_meta)
Best,
Phil
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