Venn / Euler diagrams

[swalsh]

Dear KNIME Gurus,

Looking for a node to generate Venn / Euler diagrams for two plus sets.

Saw that this was previously requested by another forum user.

Will this functionality be developed in future or is such a node available with a cryptic name (sorry but could not find it)?

Thanks and regards.

Sean

[ScottF]

Hello @swalsh -

Right now we don’t have a node that generates Venn diagrams directly. That said, you could use VennDiagram in R or Matplotlib-venn in Python to produce them inside of an R Snippet or Python Snippet node, respectively.

[swalsh]

Hi @ScottF,

Thanks for your update and advise. Tried the R approach but then ran into this problem (fresh from the Console)

WARN Table to R 0:57:35 R Version 3.5.0 and Rserve <= 1.8-6 currently have issues preventing their full use in KNIME. A future release of R and/or Rserve may fix these issues.

Trying to compile the latest version of R and Rserve (opening a whole new can of worms: requiring Mac OSX Xcode, gfortran, gcc, dependancies, ./configure options, lib paths…etc.). Perhaps I wait for the updated R/Rserve/KNIME that play nicely together because it’s getting complex and time consuming

That said, it is still possible to run my KNIME pipeline, write data to text files and reimport with native R and make the plotting there.

Keep up the good work. Despite the issues, still enjoying the fantastic KNIME tool

Best regards,

Sean

[mlauber71]

@swalsh

Trying to compile the latest version of R and Rserve (opening a whole new can of worms: requiring Mac OSX Xcode, gfortran, gcc, dependancies, ./configure options, lib paths…etc.).

yes unfortunately that is the case. I have compiled a list to follow if you want to get R up and running with KNIME even with MacOS. Maybe you have found it.

I wanted to see if I can somehow distribute a compiled package of the Rserve but was initially too stupid to do that.

Install R alongside KNIME on Windows and MacOS

Over the last months I have collected a few entries about the installation of R alongside KNIME that contain some maybe useful hints how to overcome certain obstacles while installing them. I want to bring them together here. (If you are looking for a basic guide about how to install R in the first place you might look here or here). A few maybe unnecessary remarks upfront. Yes it takes some effort to get KNIME and R up and running but in the end you will be rewarded with the whole world of pos…

[swalsh]

Hi @mlauber71,

Thanks for reply and comments

yes unfortunately that is the case. I have compiled a list to follow if you want to get R up and running with KNIME even with MacOS. Maybe you have found it.

Can you give a link to “the list” please?

My experience: R compiled fine, Rserve 1.8-6 worked after solving a problem finding libssl.a. Needed to compile openssh, change paths etc. Gave up after Rserve refused to start, looking for libR.dylib. Frankly I am afraid of breaking my system since I am not massively experienced in OSX sys admin.

Agree that a fully functional KNIME and R integration would be very useful and appreciate it is possible given time and adequate knowledge of OSX standard setup, which package managers to use, how to supply correct paths to make, configure and R install.packages()

All the best

Sean

[mlauber71]

I toyed around with Stephan Kolassa’s “Data Scientis Venn Diagram” and R. And I could bring it to PNG, although I do not claim to have fully grasped to construct a VennGram from scratch. Maybe it can serve as an inspiration …

The list of steps to compile Rserve on MacOS is in the blog entry.

kn_example_venn_gram.knwf (554.3 KB)

[swalsh]

Hi @mlauber71,

Thanks for reply. This looks really great but no time to try your solution right now - will find time in the coming weeks. As a work around, processed in KNIME (the bulk of a workflow), wrote out data and used R to make visualisation. Soon came across limitations of both Venn and Euler diagrams! But then found the rather brilliant UpSetR package that circumvents those limitations. Happy days.

Thanks also for the list of steps to compile Rserve on MacOS. I looked on the forum previously but had not noticed the blog before. Again something I will revisit sometime soon.

Best regards,

Sean