-Brief description: This repo contains executable scripts in the R programming language and BASH code to make html tables of nearest neighbor matrices.
-Motivation: Required an easy way to create an html table for nearest neighbor matrix derived by Tanimoto tests.
-Example: The R script hwriteMoreNow.R integrates the hwriter package to print tables from an SDF via ChemmineR.
-Brief: Required R 3.0 or greater working environment, Open Babel, and R packages (ChemmineR, hwriter) To install R see:
To install Open Babel see:
to test install of Open Babel type the following in the terminal:
babel -H
How to use this:
-open an R session in the dedicated git directory and type source("hwriteMoreNow.R")
-be sure to have firefox installed for auto browser launch, otherwise open test.html for nnm table with compounds shown in each cell of the matrix.
-see the data workflow via the mindmap or associated png
The test.html is in the following form:
The columns are nearest_neighbor1, nearest_neighbor2, ...
Each row has the query compound in the first cell
Sometimes the best way to view relationships is in a table. Therefore, the Tanimoto similarity relationships of small molecules in the dataset have been calculated and used to embed compounds into html tables for quick browsing.
