Articles by dgrapov

Principal Components Analysis Shiny App

June 23, 2013 | dgrapov

I’ve recently started experimenting with making Shiny apps, and today I wanted to make a basic app for calculating and visualizing principal components analysis (PCA). Here is the basic interface I came up with. Test drive the app for yourself using the code below or  check out the the ... [Read more...]

Dynamic Data Visualizations in the Browser Using Shiny

June 16, 2013 | dgrapov

After being busy the last two weeks teaching and attending academic conferences, I finally found some time to do what I love, program data visualizations using R. After being interested in Shiny for a while, I finally decided to pull the trigger and build my first Shiny app! I wanted ... [Read more...]

Tutorial- Building Biological Networks

April 4, 2013 | dgrapov

I love networks! Nothing is better for visualizing complex multivariate relationships be it social, virtual or biological. I recently gave a hands-on network building tutorial using R and Cytoscape to build large biological networks. In these networks Nodes represent metabolites and edges can be many things, but I specifically focused ... [Read more...]

PCA to PLS modeling analysis strategy for WIDE DATA

March 2, 2013 | dgrapov

Working with wide data is already hard enough, add to this row outliers and things can get murky fast. Here is an example of an anlysis of a wide data set, 24 rows  x 84 columns. Using imDEV, written in R, to calculate and visualize a principal components analysis (PCA) on this ... [Read more...]

Data analysis approaches to modeling changes in primary metabolism

January 31, 2013 | dgrapov

[This article was first published on imDEV » R, and kindly contributed to R-bloggers]. (You can report issue about the content on this page here) Want to share your content on R-bloggers? click here if you have a blog, or here if you don't. View this document on Scribd To leave a comment for the author, please follow the link and comment on their blog: imDEV » R. offers daily e-mail updates about R news and tutorials about learning R and many other topics. Click here if you're looking to post or find an R/data-science job. Want to share your content on R-bloggers? click here if you have a blog, or here if you don't. [Read more...]

Anaerobic Stress in Seeds – A Chemical Similarity Network Story

December 31, 2012 | dgrapov

The chemical similarity network or CSN is a great tool for organizing biological data based on known biochemistry or chemical structural similarity. Here is an example CSN for visualizing metabolomic  changes (measured via GC/TOF) due to anaerobic stress in germinating seeds. In this network edges are formed for chemical ... [Read more...]

ExCytR Concept

December 1, 2012 | dgrapov

The concept is to make a GUI to provide a static and dynamic linking between data and its network representations. Static access will involve making networks based on data and metadata stored in some table or spreadsheet. Dynamic control will provide interactive access to network construction and annotation properties. Together, ... [Read more...]

Excel + Cytoscape + R = ExCytR

November 16, 2012 | dgrapov

My new project is coming along nicely and should be released early 2013. It builds on the structures developed in imDEV to link Excel, Cytoscape and R using RExcel,  RCytoscape, and CytoscapeRPC . This trio can be used to rapidly generate beautiful and  informative network representations of data. Here is an example ... [Read more...]

Discriminating Between Iris Species

August 4, 2012 | dgrapov

The Iris data set is a famous for its use to compare unsupervised classifiers. The goal is to use information about flower characteristics to accurately classify the 3 species of Iris. We can look at scatter plots of the 4 variables in the data set and see that no single variable nor ... [Read more...]
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