dgrapov’s gists

dgrapov / global.R

Last active April 13, 2022 07:58

PCA using Shiny. http://spark.rstudio.com/dgrapov/PCA/

	#check for and/or install dependencies
	need<-c("RCurl","ggplot2","gridExtra","reshape2")
	for(i in 1:length(need)){
	if(require(need[i], character.only = TRUE)==FALSE){ install.packages(need[i]);library(need[i], character.only = TRUE)} else { library(need[i],character.only = TRUE)}
	}

	if(require(pcaMethods)==FALSE){
	need<-c('Rcpp', 'rJava',
	'Matrix', 'cluster', 'foreign', 'lattice', 'mgcv', 'survival')
	for(i in 1:length(need)){

dgrapov / global.R

Last active September 30, 2022 01:58

Plotting demo using ggplot2. Check out at http://spark.rstudio.com/dgrapov/1Dplots/.

	#initialize
	library(datasets)
	library(ggplot2)

	#helper function (convert vector to named list)
	namel<-function (vec){
	tmp<-as.list(vec)
	names(tmp)<-as.character(unlist(vec))
	tmp
	}

dgrapov / InchI Key Reaction Pairs

Last active December 17, 2015 21:28

	KTVPXOYAKDPRHY-SOOFDHNKSA-N AAAFZMYJJHWUPN-TXICZTDVSA-N main RP01256
	PQGCEDQWHSBAJP-TXICZTDVSA-N AAAFZMYJJHWUPN-TXICZTDVSA-N main RP10961
	YXJDFQJKERBOBM-TXICZTDVSA-N AAAFZMYJJHWUPN-TXICZTDVSA-N trans RP11184
	ZKHQWZAMYRWXGA-KQYNXXCUSA-N AAAFZMYJJHWUPN-TXICZTDVSA-N trans RP06423
	RWKJTIHNYSIIHW-MEBVTJQTSA-N AAJODOMQIUQTFG-XAICKWAHSA-N main RP12160
	RTPWRCREAVUAOI-CGJPUGKVSA-N AAKIIQMDPGWYFD-FFZYTXIOSA-N main RP11883
	XLYOFNOQVPJJNP-UHFFFAOYSA-N AAKIIQMDPGWYFD-FFZYTXIOSA-N leave RP09015
	XLYOFNOQVPJJNP-UHFFFAOYSA-N AAMCJNYIOAHDFN-BCCCWXECSA-N leave RP09666
	AUFGTPPARQZWDO-YUZLPWPTSA-N ABCOOORLYAOBOZ-KQYNXXCUSA-N trans RP08184
	BDAGIHXWWSANSR-UHFFFAOYSA-N ABCOOORLYAOBOZ-KQYNXXCUSA-N main RP10097

dgrapov / IDEOM small list

Last active December 17, 2015 04:09

This file has been truncated, but you can view the full file.

	SMID Formula Metabolite Central Map Pathway KEGGpath KEGGid PubChem CID Lmid HMDBID MetacycID CHEBI METLIN InchiKEY Synonyms
	11 H2O H2O Central Energy Metabolism Oxidative phosphorylation__Photosynthesis__Carbon fixation__Riboflavin metabolism map00190 C00001 962 HMDB02111 WATER 5585 3194 XLYOFNOQVPJJNP-UHFFFAOYSA-N Water
	25361 C10H16N5O13P3 ATP Central Energy Metabolism Oxidative phosphorylation__Photosynthesis__Purine metabolism__Puromycin biosynthesis__Zeatin biosynthesis map00190 C00002 5957 HMDB00538 ATP 2359 95 ZKHQWZAMYRWXGA-KQYNXXCUSA-N Adenosine 5'-triphosphate
	31698 C21H27N7O14P2 NAD+ Central Energy Metabolism Oxidative phosphorylation__Glutamate metabolism__Nicotinate and nicotinamide metabolism map00190 C00003 5893 HMDB00902 NAD 7422 101 BAWFJGJZGIEFAR-NNYOXOHSSA-O NAD_Nicotinamide adenine dinucleotide_DPN_Diphosphopyridine nucleotide_Nadide
	31768 C21H29N7O14P2 NADH Central Energy Metabolism Oxidative phosphorylation map00190 C00004 439153 HMDB01487 NADH 7423 3687 BOPGDPNILDQYTO-NNYOXOHSSA-N D

dgrapov / CIRgetR.r

Created May 3, 2013 18:12

	# R interface to Chemical Identifier Resolver (CIR) by the CADD Group at the NCI/NIH
	CIRgetR<-function(id,to=c("pubchem_sid"),return.all=TRUE,progress=TRUE){
	#id needs to be one of the folowing types of structural ids "inchi","inchiKey" or "smiles"
	#to can be: smiles, names, iupac_name, cas, inchi,
	# stdinchi, inchikey, stdinchikey,
	# ficts, ficus, uuuuu, image, # here return url do not evaluate
	# mw, monoisotopic_mass,file,
	# chemspider_id
	# pubchem_sid, chemnavigator_sid, formula, chemnavigator_sid

dgrapov / KEGG RPAIRS2.r

Last active December 16, 2015 12:59

dgrapov / Andrews plots and encoding.r

Last active March 2, 2018 15:31

	#needed packages
	library(andrews)
	library(ggplot2)

	#get some data here I use "mtcars"
	data<-mtcars
	fct<-as.factor(mtcars$cyl) # factor for intial grouping


	#get andrews encoding (x and y coords)

dgrapov / max intensity mass to charge pair.r

Created April 4, 2013 21:52

Data processing script to get maximum m/z ion intensity pair from Agilent recursive analysis

	#directory (file path) where the file is
	#note make sure all \ are changed to \\ or /
	dir<-"ZZZ"
	setwd(dir) # change directory

	#name of file, should be .csv
	file.name<-"XXX.csv"

	#load data into R this assumes there is a header
	input<-read.csv(file.name, header = TRUE)

dgrapov / metabolomic network.R

Last active December 15, 2015 18:49

Tutorial code for making edge lists for biochemical and chemical similarity networks

	#load needed functions: R package in progress - "devium", which is stored on github
	source("http://pastebin.com/raw.php?i=Y0YYEBia")

	# get sample chemical identifiers here:https://docs.google.com/spreadsheet/ccc?key=0Ap1AEMfo-fh9dFZSSm5WSHlqMC1QdkNMWFZCeWdVbEE#gid=1
	#Pubchem CIDs = cids
	cids # overview
	nrow(cids) # how many
	str(cids) # structure, wan't numeric
	cids<-as.numeric(as.character(unlist(cids))) # hack to break factor

dgrapov / Orthogonal Signal Correction (OSC) for PLS models OSC-PLS (OPLS)

Last active November 28, 2023 03:28

Orthogonal Signal Correction for PLS models (OPLS)

	#see updated code base and some examples in the function "test"
	# https://github.com/dgrapov/devium/blob/master/R/Devium%20PLS%20%20and%20OPLS.r

	#Orthogonal Signal Correction for PLS models (OPLS)
	#adapted from an example in the book <a href="http://www.springer.com/life+sciences/systems+biology+an+bioinfomatics/book/978-3-642-17840-5">"Chemometrics with R by Ron Wehrens"</a>

	#this code requires the following packages:
	need.packages<-c("pls", # to generate PLS models
	"ggplot2" ) # to plot results

Dmitry Grapov dgrapov