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...]

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...]

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...]

Partial least squares projection to latent structures or PLS is one of my favorite modeling algorithms. PLS is an optimal algorithm for predictive modeling using wide data or data with  rows [Read more...]

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...]

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I was interested in modeling the relationship between the power and sample size, while holding the significance level constant (p = 0.05) , for the common two-sample t-Test. Luckily R has great support for power analysis and I found the function I was looking for in the package pwr. To calculate the power ... [Read more...]

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...]

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...]

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...]

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...]

Here is an example of a data analysis work flow supported in imDEV. This network visualization was made using CmapTools. [Read more...]