It's hard to know without a minimal reproducible example, but you
probably want scale_fill_gradient or scale_fill_gradientn.
Hadley
On Thu, Oct 28, 2010 at 9:42 AM, Struchtemeyer, Chris
<strucht at okstate.edu> wrote:> I am very new to R and don't have any computer program experience
> whatsoever. ?I am trying to generate a heatmap of the following data:
>
>
>
> ?Phylum,AI,AJT,BY,GA,Grt,Sm
> ?Acidobacteria,0.5,0.7,2.7,0.1,2.6,1.0
> ?Actinobacteria,33.7,65.1,9.7,2.0,3.9,2.1
> ?Bacteroidetes,9.7,5.6,0.7,13.2,41.1,21.6
> ?CCM11b,0.0,0.0,0.0,0.0,0.0,0.1
> ?Chlamydiae,0.1,0.1,0.0,0.0,1.0,0.2
> ?Chlorobi,0.0,0.0,0.0,0.0,0.7,1.0
> ?Chloroflexi,0.1,0.2,0.6,0.2,0.8,0.6
> ?Cyanobacteria,18.7,0.0,1.0,1.5,0.9,0.3
> ?Ellusimicrobiales,0.0,0.0,0.0,0.0,0.0,0.0
> ?Firmicutes,1.0,7.6,8.3,31.9,2.1,6.9
> ?Gemmatimonadetes,5.0,0.3,0.3,0.0,0.1,0.0
> ?GN02,0.0,0.0,0.0,0.0,0.0,0.5
> ?Nitrospirae,0.0,0.2,1.1,0.0,0.0,0.0
> ?NKB19,0.0,0.0,0.9,0.0,0.0,0.0
> ?OP8,0.0,0.1,0.0,0.0,0.0,0.0
> ?OP10,0.6,0.2,0.5,0.0,0.6,0.6
> ?Planctomycetes,0.9,0.5,6.5,2.2,2.0,2.3
> ?Alphaproteobacteria,7.8,10.7,21.8,12.2,5.3,26.8
> ?Betaproteobacteria,9.9,2.8,8.9,21.7,8.3,21.9
> ?Deltaproteobacteria,0.5,0.2,1.8,2.0,1.2,7.1
> ?Epsilonproteobacteria,0.0,0.0,0.0,0.1,0.0,0.2
> ?Gammaproteobacteria,4.0,2.5,8.0,9.4,24.7,5.4
> ?SC4,0.0,0.0,0.0,0.0,0.7,0.0
> ?SM2F11,0.0,0.0,0.0,0.0,0.2,0.0
> ?SPAM,0.0,0.1,0.0,0.0,0.1,0.1
> ?Synergistes,0.0,0.0,0.0,0.1,0.0,0.0
> ?Deinococcus-Thermus,0.0,0.0,0.0,0.0,0.0,0.0
> ?TM6,0.1,0.0,0.0,0.0,0.1,0.0
> ?TM7,0.0,0.1,0.4,0.0,0.4,0.1
> ?Verrucomicrobia,3.8,2.1,23.2,2.9,1.3,0.5
> ?WPS-2,0.0,0.0,0.1,0.0,0.0,0.0
> ?WS3,0.0,0.0,0.0,0.0,0.0,0.1
> ?Uncl Bacteria,3.7,1.2,3.7,0.4,1.9,0.8
>
> I am a microbiologist. ?What I want to do is construct a heatmap showing
the
> relative abundance of each phylum. ?The far left column of my table
contains
> all of the phylum names I observed in a set of 6 water samples and each of
> the columns to the right contains the relative abundance (%) of each phylum
> in each water sample. ?I have tried constructing a heatmap using the ggplot
> guidelines listed at the following site:
> http://learnr.wordpress.com/2010/01/26/ggplot2-quick-heatmap-plotting/
>
> I can generate a heatmap using this method, but would like to alter the
> scale. ?I would like it so that I can have a little more complex gradient
> ranging from 0% to the highest relative abundance that I observe in the
> above table (65.1%). ?The default scale I get using the link above is just
a
> relative intensity scale ranging from 1 to 5 (where white represent low
> percentages and steelblue represented high percentages). ?This is alright
> but for phyla that are present at relative abundance of less than 5% all
> appear to be white (or non-existant). ?Is there anyway to fix this? ?Any
> help would be greatly appreciated.
>
> Thanks,
>
> Chris
>
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>
--
Assistant Professor / Dobelman Family Junior Chair
Department of Statistics / Rice University
http://had.co.nz/