Dear Mr. or Mrs., Please see the previous messages for information. I had a problem with the heatmap.2 breaks argument and was wondering if someone could help me with that problem. I could not find information for the other authors of heatmap.2 to contact them. Could you provide help or contact information? Best regards, Florian Goetz Phd candidate Woods Hole Oceanographic Institution 508 289 3715 -------- Weitergeleitete Nachricht -------- Betreff: RE: Heatmap.2 Breaks argument Datum: Fri, 24 Jun 2016 13:16:53 -0400 Von: Liaw, Andy <andy_liaw at merck.com> An: fgoetz <fgoetz at whoi.edu> Hi Florian, I wrote the original version of heatmap(), but not heatmap.2(). Also, heatmap() was modified by R Core before being included into base R, and is now supported by R Core. Please contact the author of heatmap.2() first. Thanks! Best, Andy> -----Original Message----- > From: fgoetz [mailto:fgoetz at whoi.edu] > Sent: Friday, June 24, 2016 10:21 AM > To: Liaw, Andy > Subject: Heatmap.2 Breaks argument > > Dear Mr. Liaw, > > I am a Phd student at the Woods Hole Oceanographic Institution, MA, USA. > I found a problem with the breaks argument in the Heatmap.2 function, > which I dont understand. When I create a Heatmap with the following code > I have trouble to open the pdf because it takes a long time to load the > Histogram. When I leave out the break argument I have no problem at all. > Why is the break argument giving me this problem. I could not find any > information on that problem so I decided to write to you directly. > > Thank you very much for any help! > > Best regards, > > Florian Goetz > > value_breaks > <-c(seq(0,0.0001,length=1),seq(0.0002,3,length=10),seq(3.01,6.5,length=10)) > ### color breaks > > my_palette<-colorRampPalette(c("white","darkblue","yellow"), > (n=length(value_breaks)-1))# > > > pdf(file.choose(new=TRUE),width=5,height=10) > #par(oma=c(2, 2, 2, 2)) > par(mar=c(20,10,15,5)) > > > heatmap.2(heatmapmatrix, > breaks=value_breaks, > symm=FALSE,trace="none", > col = my_palette,cexRow=0.5,cexCol=1,srtCol=45, > margins=c(10,8), > hclustfun = function(x) hclust(x,method = 'ward.D'), > distfun = function(x) vegdist(x,method = 'euclidean')) > > > > dev.off() #Close the pdf fileNotice: This e-mail message, together with any attachme...{{dropped:15}}
Did you try the maintainer() function? -- Sent from my phone. Please excuse my brevity. On June 24, 2016 10:45:07 AM PDT, fgoetz <fgoetz at whoi.edu> wrote:>Dear Mr. or Mrs., > >Please see the previous messages for information. I had a problem with >the heatmap.2 breaks argument and was wondering if someone could help >me >with that problem. I could not find information for the other authors >of >heatmap.2 to contact them. >Could you provide help or contact information? > >Best regards, > >Florian Goetz > >Phd candidate > >Woods Hole Oceanographic Institution > >508 289 3715 > > > >-------- Weitergeleitete Nachricht -------- >Betreff: RE: Heatmap.2 Breaks argument >Datum: Fri, 24 Jun 2016 13:16:53 -0400 >Von: Liaw, Andy <andy_liaw at merck.com> >An: fgoetz <fgoetz at whoi.edu> > > > >Hi Florian, > >I wrote the original version of heatmap(), but not heatmap.2(). Also, >heatmap() was modified by R Core before being included into base R, and >is now supported by R Core. Please contact the author of heatmap.2() >first. Thanks! > >Best, >Andy > >> -----Original Message----- >> From: fgoetz [mailto:fgoetz at whoi.edu] >> Sent: Friday, June 24, 2016 10:21 AM >> To: Liaw, Andy >> Subject: Heatmap.2 Breaks argument >> >> Dear Mr. Liaw, >> >> I am a Phd student at the Woods Hole Oceanographic Institution, MA, >USA. >> I found a problem with the breaks argument in the Heatmap.2 function, >> which I dont understand. When I create a Heatmap with the following >code >> I have trouble to open the pdf because it takes a long time to load >the >> Histogram. When I leave out the break argument I have no problem at >all. >> Why is the break argument giving me this problem. I could not find >any >> information on that problem so I decided to write to you directly. >> >> Thank you very much for any help! >> >> Best regards, >> >> Florian Goetz >> >> value_breaks >> ><-c(seq(0,0.0001,length=1),seq(0.0002,3,length=10),seq(3.01,6.5,length=10)) >> ### color breaks >> >> my_palette<-colorRampPalette(c("white","darkblue","yellow"), >> (n=length(value_breaks)-1))# >> >> >> pdf(file.choose(new=TRUE),width=5,height=10) >> #par(oma=c(2, 2, 2, 2)) >> par(mar=c(20,10,15,5)) >> >> >> heatmap.2(heatmapmatrix, >> breaks=value_breaks, >> symm=FALSE,trace="none", >> col = my_palette,cexRow=0.5,cexCol=1,srtCol=45, >> margins=c(10,8), >> hclustfun = function(x) hclust(x,method = 'ward.D'), >> distfun = function(x) vegdist(x,method = 'euclidean')) >> >> >> >> dev.off() #Close the pdf file > >Notice: This e-mail message, together with any >attachme...{{dropped:15}} > >______________________________________________ >R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >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.
Please use Reply-All to keep the mailing list included in the conversation. I don't do private consulting via the Internet, and others can correct me if I give bad advice. I doubt the maintaner function "doesn't work"... more likely you did not read the help file to learn how to use it: ?maintainer and tried to give it the name of a function instead of the name of the package containing that function: # correct usage maintainer( "gplots" ) You can confirm which package a function like heatmap.2 is in by reading the help file for that function: ?heatmap.2 or help.search( "heatmap.2" ) if you have installed that package but not yet loaded it using library(). -- Sent from my phone. Please excuse my brevity. On June 27, 2016 7:14:01 AM PDT, fgoetz <fgoetz at whoi.edu> wrote:>Hi Jeff, > >I just tried the maintainerfunction but it did not work for heatmap.2. > >Best, > >Florian > > >Am 24.06.2016 um 17:08 schrieb Jeff Newmiller: >> Did you try the maintainer() function?