Shared-control, multiple paired groups - swarmplot instead of slopegraph

[mihaela-mihaylova]

Hi,

First of all, thank you so much for the amazing package,
you've done a great job!
I am writing to you with a question about a shared-control multi-group design.
I am currently working on a project where a specific type of cells from multiple donors are stimulated with different substances
and then DE of genes is compared for the different treatment groups.
This means that, in addition to having a shared control, all the treatment groups are also paired (because the samples used are from the same set of donors across all treatment conditions).
The quantities we are interested in comparing are normalized logCPMs across conditions.

In the version which is currently on the CRAN, I am able to choose the paired = TRUE option and generate a plot which contains multiple swarmplots (one for each group), instead of a slopegraph, by just assigning slopegraph = FALSE and rawplot.type = "swarmplot" options in the plot() function.
However, I had to install the v. 0.3.9999, as the current CRAN version had a bug in the way paired difference of means was calculated. But it appears that in v. 0.3.9999 I am no longer able to generate a plot with multiple swarmplots for the groups, despite using the slopegraph = FALSE and rawplot.type = "swarmplot" options. I get a slopegraph which "connects" the points in the different conditions, which as a visualization is a little confusing, because I still want to compare
all groups to the control group only.
In the case when just one control and one treatment group are present, a swarmplot, instead of a slopegraph can still be successfully generated, using the options mentioned above.

I decided to reach out because I think that the option of having swarmplots for this shared-control multi-group paired design I described is really useful.

Thank you very much for your time and let me know if you need any clarifications!