Entering edit mode
10.2 years ago
GR
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400
Hi All,
I am plotting FPKM of my RNA-seq data in R. If on the same graph I want to highlight my gene set then what would be the best way to do this.
How I plotted the current graph:
mydata= read.table('genes_filtered.fpkm_tracking',sep="\t")
plot(density(log10(mydata$FPKM)))
Thanks.
Could you please highlight what your question is please?
Hi Michael. I have plotted FPKM of my data and as expected, got a bimodal curve. I have a gene set (~ 1000) that carry some biological property. Is it possible to highlight the FPKM of these genes in the same graph? I expect low-expression of these genes. That's why I want to show where my genes are lying in the graph.
Hope my question is bit clear now.
I think if you sort your genes according to chromosomal co-ordinates and then make a density plots along the chromosomes. It would be easier to annotate your selective genes in the plots over chromosomes
Perhaps you could put a density plot of the selected gene set above/below the entire gene set. Alternatively, just plot both and then use use partial transparency (this can be difficult to see though).
This kind of depends entirely on how you want to represent that. You could just use points() and subset your FPKM data and give your genes of interest some predefined Y offset. But without knowing what you want things to look like it'd be impossible to give you a real answer.