I am working my way through the "RNA-Seq workflow: gene-level exploratory analysis and differential expression" sample workflow using the sample data included in that workflow.

I have reached the point where the workflow document shows some graphical output such as PLOTS or HEAT MAPS.  All of the previous steps in the workflow have worked, but when I enter any commands which should be displaying some graphical output, nothing shows up in the RGui window.  Is there something I need to be doing to see the Plots or Heat Map graphical displays ?

Below is some sample code pasted from my RGui window when I enter these commands:

> par( mfrow = c( 1, 2 ) )
> dds <- estimateSizeFactors(dds)
> plot( log2( 1 + counts(dds, normalized=TRUE)[ , 1:2] ),
+      col=rgb(0,0,0,.2), pch=16, cex=0.3 )
>
> plot( assay(rld)[ , 1:2],
+      col=rgb(0,0,0,.2), pch=16, cex=0.3 )
>

I expected to see the same plots displayed on the screen, that were shown in the workflow documentation, however there was no graphical output at all. It just prompted me with ">' for the next command.

Another example is:

> library("RColorBrewer")
> sampleDistMatrix <- as.matrix( sampleDists )
> rownames(sampleDistMatrix) <- paste( rld$dex, rld$cell, sep="-" )
> colors <- colorRampPalette( rev(brewer.pal(9, "Blues")) )(255)
> hc <- hclust(sampleDists)
>
> heatmap.2( sampleDistMatrix, Rowv=as.dendrogram(hc),
+           symm=TRUE, trace="none", col=colors,
+           margins=c(2,10), labCol=FALSE )
>

Any help would be appreciated, as I am new to this.

Thanks, Greg

This is probably not a Bioconductor question. However, if you restart your Rgui and then type

plot(1:10)

Do you not get a plot? If not, you should bring this issue up over at R-help (r-help@r-project.org).

Thanks James.  I started a new RGui and typed plot(1:10).  At first nothing appeared to happen.  But then I discovered that it had opened a new window (within the RGui window), but it was behind the window that I was typing in.  When I minimized the window I was typing in, I could see the plot window behind it.  After that, when I entered a Plot command, the separate plot window now appears to be showing on top of the window I am typing in, which it now pushes to the background.  It is a bit inconsistent, but now I know that the plot comes up in a separate window, I will be able to find it.

Thanks again for your help.

Greg