Dmitry Grapov dgrapov
dgrapov
/ Andrews plots and encoding.r
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March 2, 2018 15:31
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| #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
/ KEGG RPAIRS2.r
Last active
December 16, 2015 12:59
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| C00005 C00006 | |
| C00003 C00004 | |
| C00002 C00008 | |
| C00019 C00021 | |
| C00007 C00027 | |
| C00010 C00024 | |
| C00002 C00020 | |
| C00002 C00013 | |
| C00002 C00009 | |
| C00015 C00029 |
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| # 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
/ IDEOM small list
Last active
December 17, 2015 04:09
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| 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
/ InchI Key Reaction Pairs
Last active
December 17, 2015 21:28
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| 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
/ global.R
Last active
September 30, 2022 01:58
Plotting demo using ggplot2. Check out at http://spark.rstudio.com/dgrapov/1Dplots/.
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| #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
/ global.R
Last active
April 13, 2022 07:58
PCA using Shiny.
http://spark.rstudio.com/dgrapov/PCA/
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| #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
/ query PubMed
Last active
December 19, 2015 00:48
Check for key word in PubMed article titles
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| #Check pubmed article titles for a given year for a keyword (using partial matching). | |
| library(XML) | |
| library(stringr) | |
| #get PubMed Ids for all journals for a given year | |
| getPubMedIds<-function(year=2013, max=100){ | |
| #max = maximum results to return | |
| url<-paste0("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=",year,"[PDAT]&RetMax=",max) |
dgrapov
/ server.r
Last active
October 24, 2016 12:43
Testing Shiny input text area. Based on http://stackoverflow.com/questions/14452465/how-to-create-textarea-as-input-in-a-shiny-webapp-in-r.
Need to put .js in www folder.
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| shinyServer(function(input, output, session) { | |
| inputTextarea <- function(inputId, value="", nrows, ncols) { | |
| tagList( | |
| singleton(tags$head(tags$script(src = "textarea.js"))), | |
| tags$textarea(id = inputId, | |
| class = "inputtextarea", | |
| rows = nrows, | |
| cols = ncols, | |
| as.character(value)) | |
| ) |
dgrapov
/ server.R
Last active
December 20, 2015 14:29
— forked from jknowles/server.R
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| # Script to demonstrate distributions | |
| library(VGAM) | |
| library(eeptools) | |
| library(shiny) | |
| library(ggplot2) | |
| shinyServer(function(input,output){ |