Make biplot using ggplot.

Principal Component Analysis (PCA) is a statistical procedure that uses an orthogonal transformation to convert a set of observations of possibly correlated variables into set of values of linearly un correlated variables. (from wiki) R can preform PCA very simple command “prcomp”. The result can visualise using biplot function. ggplot2 is a plotting system forContinue reading “Make biplot using ggplot.”


Try to subshape alignment

Molecular shape based alignment is useful for VS, scaffold hopping, etc. ROCS is very popular tool to do it. But there are some another tools. I found nice reference on web, and tried to do subshape alignment using RDKit. My try was failed because it took very long time ;-(. This is snippet.. ” IContinue reading “Try to subshape alignment”

Make graph with python

Visualization of data is very important. Some years ago, I was interested in cytoscape to visualize molecular network (a.k.a. similarity, MMP, etc.). But it was difficult to integrate python script. Today, I found cool python library “d3py”. It can get from github ;-). “” This library can make any graphs easy like ggplot, vincent andContinue reading “Make graph with python”