plot module

[mschubert]

Task list before merge into develop

Consider what's implemented in the ggfortify, GGally, ggdendro, ggRandomForests, and ggmcmc packages.

• [x] color
  • [x] gradients
  • [x] generating from color map
  • [x] plotting of gradients
  • [x] quantization
  • [x] categorical
  • [x] categorical + continuous
• [x] label
• [ ] matrix
  • [x] full
  • [ ] upper/lower triangular
• [ ] heatmap
  • [x] pheatmap interface that respects df conventions
• [x] venn
  • [x] start from list of vectors
  • [x] size-proportional
  • [x] tree plots?
• [ ] linear_fit
  • [x] linear associations
  • [ ] p-value reporting
  • [ ] rsquared reporting
• [x] volcano
  • [x] coloring according to effect direction and p-value

[klmr]

I’d like to avoid introducing inconsistencies if possible (don’t know what the status of this is). For instance, plotrix, heatmap.2 etc just do it objectively wrong.

We should try really, really hard to create APIs compatible with ggplot’s grammar of graphics, and with tidy data.

[mschubert]

We should try really, really hard to create APIs compatible with ggplot’s grammar of graphics, and with tidy data.

This is exactly what I'm trying to do.

However, there is things that ggplot2 can't easily do, like having the clustering tree next to the main plot. We'll have to find an acceptable solution for this. Options, as I see it, are (a) create an interface to pheatmap that takes the same structure as ggplot2 would and (b) teach ggplot2 about trees somehow.

[klmr]

There’s ggdendro. No idea how well that works. And I’ve just found plot_tree, which also looks interesting.

[mschubert]

ggally might also be something to look at

[barzine]

While you are working on this, can you also integer the options of heatmap3 (https://github.com/slzhao/heatmap3) for the annotation. Even, if I have to override some part of the function (and Nuno has also his own improved version) this package gives a nice overview of what I mean (http://www.biomedcentral.com/1471-2105/15/S10/P16/figure/F1) (I have a start of something myself, but I never come around to finish it yet)

[jergosh]

Greg Jordan wrote some ggplot-based code for plotting trees for Phylosim, if anyone feels like rolling their own and would like inspiration.

GregS

On Thu Feb 19 2015 at 10:08:32 AM M.P. Barzine notifications@github.com wrote:

While you are working on this, can you also integer the options of heatmap3 (https://github.com/slzhao/heatmap3) for the annotation. Even, if I have to override some part of the function (and Nuno has also his own improved version) this package gives a nice overview of what I mean ( http://www.biomedcentral.com/1471-2105/15/S10/P16/figure/F1)

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