[BioC] cummerbund how to get matrix for csheatmap

[Loyal Goff]

To follow up, there also exists an fpkmMatrix() method to reshape the fpkm results into a feature X condition matrix, e.g.:

fpkmMatrix(myGenes)

Cheers,
Loyal

On Mar 5, 2013, at 11:17 PM, Valerie Obenchain <vobencha at fhcrc.org> wrote:

> Hi Adrian,
> 
> If we follow the example in the vignette we eventually get to these lines which I think are similar to what you are showing below.
> 
> From vignette:
> ...
> 
> data(sampleData)
> myGeneIds<-sampleIDs
> myGeneIds
> myGenes<-getGenes(cuff,myGeneIds)
> myGenes
> head(fpkm(myGenes))
> h<-csHeatmap(myGenes,cluster='both')
> 
> 
> To get the data plotted in csHeatmap() you'll want to look inside the the 'myGenes' object.
> 
> > myGenes
> CuffGeneSet instance for  20  genes
> 
> Slots:
>     annotation
>     fpkm
>     repFpkm
>     diff
>     count
>     isoforms     CuffFeatureSet instance of size 45
>     TSS         CuffFeatureSet instance of size 23
>     CDS         CuffFeatureSet instance of size 36
>     promoters         CuffFeatureSet instance of size 20
>     splicing         CuffFeatureSet instance of size 23
>     relCDS         CuffFeatureSet instance of size 20
> 
> Each of the slots has an accessor and I think fpkm() is what your are looking for.
> 
> > head(fpkm(myGenes))
>      gene_id sample_name        fpkm     conf_hi  conf_lo quant_status
> 1 XLOC_000069 Fibroblasts 2.05083e-01 8.94501e-01 0.000           OK
> 2 XLOC_000069        hESC 1.77686e+02 2.15888e+02 139.484           OK
> 3 XLOC_000069         iPS 1.90000e+01 3.88149e+01 0.000           OK
> 4 XLOC_000089 Fibroblasts 1.39701e+04 2.19187e+04 6021.450           OK
> 5 XLOC_000089        hESC 7.18339e+03 7.92296e+03 6443.810           OK
> 6 XLOC_000089         iPS 1.41690e+03 1.96558e+03 868.215           OK
>        stdev
> 1    0.344709
> 2   19.101000
> 3    9.907450
> 
> 
> Valerie
> 
> 
> On 03/01/13 10:05, Adrian Johnson wrote:
>> Hi:
>> I am trying to plot the most significant genes. I have 3 different
>> sample types and 4 replicates each. Could anyone suggest how do I get
>> the matrix of fpkm values that was plotted in csHeatmap function.
>> 
>>> diffGeneIDs <- getSig(cuff,level="genes",alpha=0.001)
>>> diffGenes<-getGenes(cuff,diffGeneIDs)
>>> h<-csHeatmap(diffGenes,cluster='both')
>> 
>> the heatmap gene names are not visible. I want to get the matrix for h
>> and plot heatmap using another heatmap function.
>> How do I get the matrix for h.
>> 
>> thanks
>> Adrian
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>>> sessionInfo()
>> R version 2.15.2 (2012-10-26)
>> Platform: i386-w64-mingw32/i386 (32-bit)
>> 
>> locale:
>> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
>> States.1252    LC_MONETARY=English_United States.1252
>> [4] LC_NUMERIC=C                           LC_TIME=English_United
>> States.1252
>> 
>> attached base packages:
>> [1] grid      stats     graphics  grDevices utils     datasets
>> methods   base
>> 
>> other attached packages:
>>  [1] cummeRbund_2.0.0     Gviz_1.2.1           rtracklayer_1.18.2
>> GenomicRanges_1.10.7 IRanges_1.16.6       fastcluster_1.1.8
>> reshape2_1.2.2
>>  [8] ggplot2_0.9.3        RSQLite_0.11.2       DBI_0.2-5
>> BiocGenerics_0.4.0
>> 
>> loaded via a namespace (and not attached):
>>  [1] AnnotationDbi_1.20.4   Biobase_2.18.0         biomaRt_2.14.0
>>    Biostrings_2.26.3      biovizBase_1.6.2       bitops_1.0-5
>>  [7] BSgenome_1.26.1        cluster_1.14.3         colorspace_1.2-1
>>    dichromat_2.0-0        digest_0.6.3
>> GenomicFeatures_1.10.2
>> [13] gtable_0.1.2           Hmisc_3.10-1           labeling_0.1
>>    lattice_0.20-13        MASS_7.3-23            munsell_0.4
>> [19] parallel_2.15.2        plyr_1.8               proto_0.3-10
>>    RColorBrewer_1.0-5     RCurl_1.95-3           Rsamtools_1.10.2
>> [25] scales_0.2.3           stats4_2.15.2          stringr_0.6.2
>>    tools_2.15.2           XML_3.95-0.1           zlibbioc_1.4.0
>> 
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>