[BioC] help with ReportingTools

[James W. MacDonald]

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
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099