Hi, I have a CSV file with various biological reactions. Subscripts, superscripts, and italics are encoded in carats, and I was wondering if R can actually recognize those and print actual superscripts, etc. Here's an example: <i>S</i>-adenosyl-L-methionine + rRNA = <i>S</i>-adenosyl-L-homocysteine + rRNA containing <i>N<sup>6</sup></i>-methyladenine Thanks, -Nina
Hi Nina,> Subscripts, superscripts, and italics are encoded in carats, and I was > wondering > if R can actually recognize those and print actual superscripts, etc. > Here's an example:I know that ladies are fond of diamonds (perhaps you mean carets?); though it isn't quite clear what you want (though we do know what ...). Can R do superscripts, subscripts and all the other plotmath stuff? Yes, very much so; but it still isn't clear what your real question is. See ?plotmath, in any event. HTH, Mark. naw3 wrote:> > Hi, > > I have a CSV file with various biological reactions. Subscripts, > superscripts, > and italics are encoded in carats, and I was wondering if R can actually > recognize those and print actual superscripts, etc. Here's an example: > > S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + > rRNA containing N<sup>6</sup>-methyladenine > > Thanks, > -Nina > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > >-- View this message in context: http://www.nabble.com/Decoding-subscripts-superscripts-from-CSVs-tp18598344p18598727.html Sent from the R help mailing list archive at Nabble.com.
On Tue, 2008-07-22 at 16:18 -0400, naw3 at duke.edu wrote:> Hi, > > I have a CSV file with various biological reactions. Subscripts, superscripts, > and italics are encoded in carats, and I was wondering if R can actually > recognize those and print actual superscripts, etc. Here's an example: > > <i>S</i>-adenosyl-L-methionine + rRNA = <i>S</i>-adenosyl-L-homocysteine + > rRNA containing <i>N<sup>6</sup></i>-methyladenine >Hi Nina, Embedded formatting commands enclosed in angle brackets (a caret is ^) are almost certainly from the SGML family of markup languages and probably from XML as this is becoming more common as a data format. If you want to translate the XML to plotmath, you must change the XML tags to plotmath tags. Here is a toy function for your example: xml2pm<-function(xmlstring) { xmlstring<-gsub("<[iI]>","italic(",xmlstringE) xmlstring<-gsub("</[Ii]>",")",xmlstring) xmlstring<-gsub("<[Ss][Uu][Pp]>","^",xmlstring) xmlstring<-gsub("</[Ss][Uu][Pp]>","",xmlstring) return(xmlstring) } Jim