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@NoahHenrikKleinschmidt NoahHenrikKleinschmidt released this 12 Mar 11:26
· 301 commits to main since this release
v.3.1.2
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Learn about vigilant mode.

This update introduces support for new pre-implemented normalisation methods as well as new Plotters.

Normalisation mode

Up to now the Normaliser by default strictly paired replicates by their order (1st - 1st, 2nd - 2nd, etc.). In addition to this pair-wise normalisation, two new normalisation modes are now available to account for equivalence between replicates in cases where they were pipetted separately and there is no strict reason to link replicates in such a fashion. These modes are combinatoric, which computes combinations of 1st-1st, 1st-2nd etc., and permutative, which approximates combinatoric computation through iterative permutations in cases where datasets may be large and combinatoric computation is therefore undesired.

Dot Plots

New Plotters are introduced that show the individual normalised fold changes in dot plots rather than as mean + stdev. Optionally, violins can be added to aid visualising the distribution. New Plotters implemented for this are AssayDots and GroupDots.

Group-Plotters and Assay-Plotters

Up to now, by default separate assays were displayed in separate subplots, with the replicate groups plotted on the x-axis. Now, another option is introduced wherein the separate groups are displayed in subplots and assays on the x-axis. The two grouped-kind Plotters are GroupBars and GroupDots, which visualise the results either in bar charts or as dot plots. Their equivalents are AssayBars (which is the same as the default PreviewResults) and AssayDots.

More versatile PreviewResults

To allow more easy interaction with the new plotters, PreviewResults is now a wrapper that can call on any Plotter that displays a preview of the results: AssayBars, AssayDots, GroupBars, GroupDots. AssayBars has now taken over the core role that was previously held directly by PreviewResults and this is now the default mode, so the main behaviour of PreviewResults remains unchanged.

Filter-NaN

A bug was fixed that caused Filters to crash when encountering all-NaN groups. Also, Filters now by default set outliers to NaN instead of completely removing the entries (this behaviour can be changed, however).

FilterSummary Class

A new Plotter dedicated to visualising Filtering is now available and replaces the previous setup of two consecutive ReplicateBoxPlots. The new FilterSummary figure displays separate assays in separate subplots and offers two boxes for each replicate group next to each other, one showing the data pre-filtered and one post-filtered. �

Bugfixes

Some other small bugs were fixed as they were discovered.

Assets 3
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