On Wed, Feb 4, 2009 at 3:57 AM, hemant ritturaj <ritturajhemant@gmail.com>wrote:

> Dear all,
>
> Thanks for the kind suggestion
> I used the with my data in the following way
>
>
> heatmap.2(x,col=redgreen(75),Rowv=TRUE,Colv=FALSE,scale="row",key=FALSE,symkey=FALSE,
> density.info
> ="none",labRow=Y,labCol=c("control","stress"),trace="none",cexRow=0.5,margin=c(10,10),lhei=c(0.5,1),
> lwid=c(0.5,1),cexCol=1)
>
> But the problem is, i want to control cell width and I am not able to do
> with the mentioned command.
>
> And Also i want to increase the colour variation so that it can pick even
> very small changes in the values.
> Regards


You'll want to look at the breaks argument.  There are also a number of
posts in the archives about this issue.

Sean



>
>
> On Tue, Feb 3, 2009 at 3:10 AM, James W. MacDonald <jmacdon@med.umich.edu
> >wrote:
>
> > Hi Hemant,
> >
> > Does this help?
> >
> > > library("gplots")
> > > z <- matrix(rnorm(600), ncol=6)
> > >
> >
> heatmap.2(z)heatmap.2(x,col=redgreen(75),Rowv=TRUE,Colv=FALSE,scale="row",key=FALSE,symkey=FALSE,
> > density.info
> ="none",labRow=Y,labCol=c("control","stress"),trace="none",cexRow=0.5,margin=c(10,10),lhei=c(0.5,1),
> > lwid=c(0.5,1),cexCol=1)
> > > heatmap.2(z, lhei=c(0.5,1), lwid=c(0.5,1), key=FALSE)
> > > heatmap.2(z, lhei=c(0.5,3), lwid=c(0.5,3), key=FALSE)
> > > heatmap.2(z, lhei=c(0.5,4), lwid=c(0.5,3), key=FALSE)
> >
> > And yes, you can get the error that figure margins are too large if you
> use
> > extreme values for lhei and lwid.
> >
> >
> > Best,
> >
> > Jim
> >
> > hemant ritturaj wrote:
> >
> >> Dear All,
> >>
> >> Thanks for kind help.
> >>
> >> But I am really not able to understand the way it used. Can any plz help
> >> in
> >> understanding the way it is used, as when i used the way it is given on
> >> manual page, it said figure is beyond the margins.....
> >>
> >> Also I want to reduce the size of the tree in the heatmap.
> >>
> >> I shall be very thankful for your kind help
> >>
> >> On Sat, Jan 31, 2009 at 12:27 AM, James W. MacDonald
> >> <jmacdon@med.umich.edu>wrote:
> >>
> >>  Hi Hemant,
> >>>
> >>> I think you want to read about the arguments 'lhei' and 'lmat',
> >>> specifically in the last paragraph of the details section of
> ?heatmap.2.
> >>> You
> >>> will also likely want to look at ?layout, which is what these arguments
> >>> control.
> >>>
> >>> Best,
> >>>
> >>> Jim
> >>>
> >>>
> >>>
> >>>
> >>> hemant ritturaj wrote:
> >>>
> >>>  Dear All
> >>>>
> >>>> I was trying to make a heatmap using library(gplots)
> >>>>
> >>>> library("gplots")
> >>>> t <-(read.table("target_file",header=TRUE))
> >>>> Y <-t$ID
> >>>> x<-as.matrix(t[2:7])
> >>>>
> >>>>
> >>>>
> heatmap.2(x,col=redgreen(75),Rowv=TRUE,Colv=TRUE,scale="row",key=TRUE,symkey=FALSE,
> >>>> density.info
> >>>>
> >>>>
> >>>>
> ="none",labRow=Y,labCol=c("control","control","control","stress","stress","stress"),trace="none",cexRow=0.5)
> >>>>
> >>>> My problem is, it plots a heatmap which looks very odd, I want to
> >>>> control
> >>>> the size of box it make in heatmap.
> >>>>
> >>>> Using margin=c(12,12) in the function reduces the picture as a whole
> but
> >>>> not
> >>>> the size of boxes it makes.
> >>>>
> >>>> Can anyone help me making the pretty heatmap
> >>>>
> >>>> I shall be very thankful for your kind help
> >>>>
> >>>> Regards
> >>>>
> >>>>
> >>>>  --
> >>> James W. MacDonald, M.S.
> >>> Biostatistician
> >>> Hildebrandt Lab
> >>> 8220D MSRB III
> >>> 1150 W. Medical Center Drive
> >>> Ann Arbor MI 48109-0646
> >>> 734-936-8662
> >>>
> >>>
> >>
> >>
> >>
> > --
> > James W. MacDonald, M.S.
> > Biostatistician
> > Hildebrandt Lab
> > 8220D MSRB III
> > 1150 W. Medical Center Drive
> > Ann Arbor MI 48109-5646
> > 734-936-8662
> >
>
>
>
> --
> Hemant Ritturaj Kushwaha
> PhD Student
> Center for Computational Biology and Bioinformatics
> Jawaharlal Nehru University
> New Delhi-110067
> Phone: 09868801604
>
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>
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