[R] Fwd: Fwd: RE: Heatmap.2 Breaks argument

[fgoetz]

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

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