Thanks Martin. Very useful. can you plot multiple lanes with different colors in one graph?
________________________________ From: Martin Morgan <[email protected]> Cc: Steve Lianoglou <[email protected]>; [email protected] Sent: Sun, August 22, 2010 12:55:08 PM Subject: Re: [Bioc-sig-seq] read length distribution from ShortReadQ or AlignedRead On 08/22/2010 11:32 AM, joseph wrote: > Perfect. Thanks. a little tangential, but plot(table(width(reads))) avoids the arbitrary histogram bins when the number of unique values of width(reads) is small, and library(lattice); densityplot(width(reads), plot.points=FALSE) avoids the arbitrary choice of bin widths when the number of unique values of width(reads) is large. Martin > > > > > ________________________________ > From: Steve Lianoglou <[email protected]> > > Cc: [email protected] > Sent: Sun, August 22, 2010 10:59:37 AM > Subject: Re: [Bioc-sig-seq] read length distribution from ShortReadQ or > AlignedRead > > Sorry .. didn't CC to bioc (like I told you to do :-) ... > > On Sun, Aug 22, 2010 at 1:58 PM, Steve Lianoglou > <[email protected]> wrote: >> Hi Joseph, >> >> Don't forget to hit "Reply All" when responding to BioC emails, so >> that the help stays on the list .. >> > >>> Thanks Steve. >>> how do I get a table of the actual values? >> >> The `width` function returns a vector of the same length as your >> ShortRead object (which is the number of reads you have there), so >> assuming your ShortRead object is still called `reads`: >> >> R> read.length <- width(reads) >> >> That `read.length` vector has the length of all the reads. You can >> then manipulate it as you would any other vector in R. It sounds like >> you might want the `table` or `tabulate` function, or something >> similar. >> >> Also note that the `hist` function returns an "invisible" object you >> can work with. If you do something like this: >> >> R> h <- hist(width(reads)) >> >> `h` might look something like this: >> >> R> h >> $breaks >> [1] 30 40 >> >> $counts >> [1] 256 >> >> $intensities >> [1] 0.1 >> >> $density >> [1] 0.1 >> >> $mids >> [1] 35 >> >> $xname >> [1] "width(rfq)" >> >> $equidist >> [1] TRUE >> >> attr(,"class") >> [1] "histogram" >> >> -steve >> >> -- >> Steve Lianoglou >> Graduate Student: Computational Systems Biology >> | Memorial Sloan-Kettering Cancer Center >> | Weill Medical College of Cornell University >> Contact Info: http://cbio.mskcc.org/~lianos/contact >> > > > -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
