[BioC] help with ReportingTools

[Abhishek Pratap]

Just for completeness...after updating to the latest versions it works well.

I now have other specific questions with regards to page formatting
with ReportingTools. I will start another specific thread for the
same.

Cheers!
-Abhi

On Mon, Jun 17, 2013 at 10:37 AM, Abhishek Pratap <apratap at lbl.gov> wrote:
> 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