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 >>> >>> _______________________________________________ >>> 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 >> > > > Ok thanks Jim..this calls for an upgrade for sure. > > -Abhi