Waterfall plots are a common visualization method to view multiple spectra and have some similarities with joy plots. In the high throughput screening world, people have plot multiple dose response curves, offset on the z-axis to produce something that looks like a waterfall. An example is Figure 1 in Inglese et al, PNAS, 2006, 103(31). […]
Ridit Analysis
While preparing material for an R workshop I ran at NCATS I was pointed to the topic of ridit analysis. Since I hadn’t heard of this technique before I decided to look into it and investigate how R could be used for such an analysis (and yes, there is a package for it). Why ridit […]
Summarizing Collections of Curves
I was browsing live notes from the recent IEEE conference on visualization and came across a paper about functional boxplots. The idea is an extension of the boxplot visualization (shown alongside), to a set of functions. Intuitively, one can think of a functional box plot as specific envelopes for a set of functions. The construction […]
fingerprint 3.5.2 released
Version 3.5.2 of the fingerprint package has been pushed to CRAN. This update includes a contribution from Abhik Seal that significantly speeds up similarity matrix calculations using the Tanimoto metric. His patch led to a 10-fold improvement in running time. However his code involved the use of nested for loops in R. This is a well […]
Updated version of rcdk (3.2.3)
I’ve pushed updates to the rcdklibs and rcdk packages that support cheminformatics in R using the CDK. The new versions employ the latest CDK master, which as Egon pointed out has significantly fewer bugs, and thanks to Jon, improved performance. New additions to the package include support for the LINGO and Signature fingerprinters (you’ll need the […]