Hello,
I have 2 datasets
1) GWAS summary stats with pvalues for a selected region
2) Expression data with pvalues for the same selected region
Both the datasets are in the following format in two columns and approx 2000-3000 rows chr:position pvalue
I want to visualize a scatter plot by overlaying the pvalues from both datasets and also include gene names (a plot that may look similar to locuszoom). I am not sure what packages would be appropriate for to generate such plots ?
Thank you.
and this would also annotate gene names to the plot ?
Annotating them is up to you, plotting them is then simple. Of course annotating regions isn't difficult assuming you have an annotation file somewhere.
great, many thanks... I'll give this a shot !