[BioC] help with ReportingTools

[Abhishek Pratap]

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")

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