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.”

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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 ;-). “https://github.com/mikedewar/d3py” This library can make any graphs easy like ggplot, vincent andContinue reading “Make graph with python”