[BioC] cummerbund how to get matrix for csheatmap

[Adrian Johnson]

Thank you Valerie and Loyal. That was helpful.
Adrian

On Tue, Mar 5, 2013 at 11:24 PM, Loyal Goff <lgoff at csail.mit.edu> wrote:
> 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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>>
>