[BioC] help with ReportingTools

[Abhishek Pratap]

On Mon, Jun 17, 2013 at 8:13 AM, James W. MacDonald <jmacdon at uw.edu> wrote:
> Hi Abhi,
>
>
> On 6/16/2013 6:50 PM, Abhishek Pratap wrote:
>>
>> Hi
>>
>> I seem to be getting an error when trying to replicate ReportingTools
>> example of putting a plot on the webpage both using the one generated
>> in R and an external image. Not sure if the error has anything to do
>> with versions. Session info included too.
>>
>>
>>
>> ###
>> #plot generated within R
>> ###
>> my.df<- data.frame(EGID = c("103", "104", "105", "106", "107"),
>>                      RPKM = c(4, 5, 3, 100, 75),
>>                      DE = c("Yes", "Yes", "No", "No", "No"))
>>
>> plot(my.df$EGID, my.df$RPKM, xlab="EGID",ylab="RPKM", main="Scatter
>> plot of RPKMs", col="blue")
>> scatterPlot<- recordPlot()
>> library(lattice)
>> barPlot<- barchart(my.df$RPKM~my.df$EGID) ##lattice plots behave
>> slightly differently
>> htmlRep3<- HTMLReport(shortName = "my_html_file3", title="Adding a
>> plot directly to the page",reportDirectory = "./reports")
>> publish(scatterPlot, htmlRep3, name = "scatterPlot")
>
>
> You are using the vignette for ReportingTools 2.0.1, but are running
> ReportingTools 1.0.0. There have been wholesale changes in ReportingTools
> between these versions, so a large portion of the code that would work with
> 1.0.0 will no longer do so.
>
> You should upgrade to R-3.0.1 and BioC 2.12 and then try again.
>
> Best,
>
> Jim
>
>
>>
>> Error in as(object, "data.frame") :
>>    no method or default for coercing “recordedplot” to “data.frame”
>>
>>
>> #####
>> ****Also when I try to put a pre-generated image***
>> #####
>> himg<- hwriteImage("scatterplot.png")
>> publish(hwrite(himg,br=TRUE)
>>
>> Error in as(object, "data.frame") :
>>    no method or default for coercing “character” to “data.frame”
>>
>>
>>
>> Thanks!
>> -Abhi
>>
>>> sessionInfo()
>>
>> R version 2.15.2 (2012-10-26)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>>
>> locale:
>>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>> LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>> LC_MONETARY=en_US.UTF-8
>>   [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=C                 LC_NAME=C
>>                 LC_ADDRESS=C               LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] hwriter_1.3          BiocInstaller_1.8.3  lattice_0.20-10
>> ReportingTools_1.0.0 AnnotationDbi_1.20.7 Biobase_2.18.0
>> BiocGenerics_0.4.0
>> [8] RSQLite_0.11.3       DBI_0.2-7
>>
>> loaded via a namespace (and not attached):
>>   [1] annotate_1.36.0       AnnotationForge_1.0.3 Category_2.24.0
>> edgeR_3.0.8           genefilter_1.40.0     GO.db_2.8.0
>> GOstats_2.24.0
>>   [8] graph_1.36.2          grid_2.15.2           GSEABase_1.20.2
>> IRanges_1.16.3        limma_3.14.4          parallel_2.15.2
>> PFAM.db_2.8.0
>> [15] RBGL_1.34.0           splines_2.15.2        stats4_2.15.2
>> survival_2.36-14      tools_2.15.2          XML_3.96-1.1
>> xtable_1.7-1
>>
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>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>


Ok thanks Jim..this calls for an upgrade for sure.

-Abhi