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