Blog Archives

Push it to the limit: SOM + Clustering + Networks

May 18, 2016
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Push it to the limit: SOM + Clustering + Networks

What is the highest dimensional visualization you can think of? Now imagine it being interactive. The following details a Frankenstein visualization packing a smorgasbord of multivariate goodness. Enter first, self-organizing maps (SOM). I first fell into a love dream with SOMs after using the kohonen package. The  wines data set example is a beautiful display of information.

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Try’in to 3D network: Quest (shiny + plotly)

April 8, 2016
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Try’in to 3D network: Quest (shiny + plotly)

I have an unnatural obsession with 4-dimensional networks. It might have started with a dream, but VR  might make it a reality one day. For now I will settle for  3D networks in Plotly. Presentation: R users group (more) More: networkly

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Network Visualization with Plotly and Shiny

February 28, 2016
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Network Visualization with Plotly and Shiny

In addition to their more common uses, networks  can be used as powerful multivariate data visualizations and exploration tools. Networks not only provide mathematical representations of data but are also one of the few data visualization methods capable of easily displaying multivariate variable relationships. The process of network mapping involves using the network manifold to display a

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Data Analysis Workflow: ‘Omics style

October 9, 2015
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Data Analysis Workflow: ‘Omics style

Follow along with the presentation and recreate all the analysis results for yourself.

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Metabolomics and Beyond: Challenges and Strategies for Next-gen Omic Analyses

September 18, 2015
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Metabolomics and Beyond: Challenges and Strategies for Next-gen Omic Analyses

Recently I had the pleasure of giving lecture for the Metabolomics Society on Challenges and Strategies for Next-gen Omic Analyses. You can check out all of my slides and video of the lecture below.

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dplyr Tutorial: verbs + split-apply-combine

May 3, 2015
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dplyr Tutorial: verbs + split-apply-combine

At a recent Saint Louis R users meeting I had the pleasure of giving a basic introduction to the awesome dplyr R package. For me, data analysis ubiquitously involves splitting the data based on grouping variable and then applying some function to the subsets or what is termed split-apply-combine. Having personally recently incorporated dplyr into

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dplyr Tutorial: verbs + split-apply

May 3, 2015
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dplyr Tutorial: verbs + split-apply

At a recent Saint Louis R users meeting I had the pleasure of giving a basic introduction to the awesome dplyr R package. For me, data analysis ubiquitously involves splitting the data based on grouping variable and then applying some function to the subsets or what is termed split-apply (typically split-lapply-apply). Having personally recently incorporated

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2014 Metabolomic Data Analysis and Visualization Workshop and Tutorials

October 11, 2014
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2014 Metabolomic Data Analysis and Visualization Workshop and Tutorials

Recently I had the pleasure of teaching statistical and multivariate data analysis and visualization at the annual Summer Sessions in Metabolomics 2014, organized by the NIH West Coast Metabolomics Center. Similar to last year, I’ve posted all the content (lectures, labs and software) for any one to follow along with at their own pace. I also

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2014 UC Davis Proteomics Workshop

August 9, 2014
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2014 UC Davis Proteomics Workshop

Recently I had the pleasure of teaching data analysis at the 2014 UC Davis Proteomics Workshop. This included a hands on lab for making gene ontology enrichment networks. You can check out my lecture and tutorial below or download all the material. Introduction Tutorial 2014 UC Davis Proteomics Workshop Dmitry Grapov is licensed under a

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PubChem 446220 = Yeyo

August 8, 2014
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PubChem 446220 = Yeyo

I just updated my R package, CTSgetR, for biological database translation using the Chemical Translation Service (CTS). While making code examples I came across some humorous chemical name synonyms for the molecule referenced in PubChem  as CID = 446220. Below are a few examples, can you guess what this is? Badrock, Bazooka, Bernice, Bernies, Blast, Blizzard, Bouncing Powder, Bump, Burese,

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