When comparing Coggle vs vimwiki plugin for vim, the Slant community recommends vimwiki plugin for vim for most people. In the question“What is the best cross-platform note-taking app?” vimwiki plugin for vim is ranked 23rd while Coggle is ranked 56th.
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Pros
Pro Supports Markdown (their own variant)
Markdown is a plain text formatting syntax designed so that it can optionally be converted to HTML using a tool by the same name.
Pro Collaborative
Coggle allows inviting friends and colleagues to work collaboratively on notes and diagrams in real-time.
Pro Pretty diagrams
No effort to create beautiful diagrams.
Pro Supports LaTeX
LaTeX is a document preparation system and document markup language. It is the de facto standard for the communication and publication of scientific documents.
Pro Allows easy color-coding of paths
Pro Versioning support
Enter history mode to view all changes to a diagram over time, and make a copy from that point.
Pro Optional Chrome store App
Pro Free
Pro Lots of export options
Exports to PDF, image, plaintext and .mm files.
Pro Internal link makes it easy to create a knowledge network
Pro Comfortable for Vim users
Has a very minimal learning curve for people already used to Vim, as the preset shortcuts are very easy to learn and don't conflict badly with other Vim behaviors.
Cons
Con Tree relations only; no non-parent links
Coggle's model allows a node to have multiple children, but only one parent, and no other connections of any sort.
Con Unconventional note taking style
Coggle is a mind mapping application, not a traditional text based note storage platform.
Con Limited to use with vim only
vimwiki is a plugin for vim, so you won't be able to make use of it if you're not a vim user (and don't want to be).