Say hi to our new responsive plots

Many graphs in R2 are now adaptable with a responsive plot options menu, that you can find with a click on a graph's gear icon. The graph immediately responds to changes in these settings. This level of interactivity enables more direct and smooth play with the plots.

The gear icon is located upper left of many graphs now.
The menu that opens upon a click of the gear icon allows to easily

• Save or copy a plot
• Interactively change the graph type (e.g. from violin to boxplot)
• Interactively customize the appearance of the elements in the plot (e.g. colors, dot and font size, orientation, mark samples)

To play around with these features, we recommend you to follow one of the chapters in our tutorial, such as our tutorial chapter on the Differential Expression between groups analysis.
For a quick instruction, we summarized the graph options below.

Save or copy a plot

When you left-click on the gear icon, a panel is shown with several tabs and various options per tab. Click on the Save tab if you want to store the image as a png or svg. Click on the copy button to place the image on the clipboard. This makes it possible to paste the image immediately in your other applications, such as Microsoft Powerpoint.

Interactively change the graph type or the appearance

Interactively change the graph type (e.g. from violin to boxplot) and customize the appearance of the elements in the plot(e.g. colors, dot and font size, orientation). A click on the gear icon will open a panel in which these extra plot settings are located on the General and the Extra tab. These settings can be adapted without the need to hit a submit button upon change.
An update button is still included in the panel to initiate a re-draw of the plot if needed.




These graphs often allow you to click on elements in the plot, to either open up the settings that belong to the element, or to mark the sample that you click on.

The volcano plot, accessible via the differential expression results page, has been updated with additional interactive features.
Lastly, legends allow you to click on a category to hide/show the sample subgroup.

Two different kind of R2 menus

To summarize, many graphs in R2 are now responsive with settings that take immediate effect upon change and with plot elements that are interactive. Besides these newer responsive settings, on most pages in R2, you will (also) still find a settings menu that allows you to change parameters of an analysis, but that requires you to submit made changes with a specific button.

Below is a picture of the two different kinds of menus that you often encounter in R2:

• The responsive plot options menu (marked in red) that appears when you hit the gear button . Changes made in these settings take immediate effect in the graph.
• The grey Adjustable settings menu (marked in green) that you often find on intermediate analysis pages and at the bottom of a result page. These menus often allow you to adjust analysis parameters and require clicking the submit button to apply changes.

Check out the R2 collaborator Bulletin 2024-01. Especially for our collaborator users.

iTHER Precision Medicine Data Scope

With the publication of langenberg et al in European Journal of Cancer titled: "Implementation of paediatric precision oncology into clinical practice: The Individualized Therapies for Children with cancer program 'iTHER'", the data presented in this manuscript is also available in R2

Use the 'iTHER (PMC)' datascope to launch the personalized medicine tools implemented in R2 and see how they have been used in tumor board sessions, to identify potentially targetable events from the profiling data generated at the DKFZ in Heidelberg Germany, or using the Genomics core of the Princes Maxima Center in Utrecht, the Netherlands.

All of these developments would heve been impossible without the feedback and suggestions of the ither entity experts and the data delivery teams at DKFZ and the PMC.

Navigate to the data scope for this resource, using the menu item and start to explore the rich data on 230 pediatric cancer cases that were included in the iTHER and iTHER2.0 studies.