The plotting character is determined by the pch argument.
i.e. You need to specify the pch argument in the legend call.
Here's the R code to preview the first 20 plotting characters:
> plot (1:20, rep (0, 20), pch=1:20, ylim = c (-5, 5) )
> text (1:20, rep (1, 20), 1:20)
Empty circles, have a pch value of 1.
Solid circles, have a pch value of 16.
In general, to set the color, use the col argument.
So, you could add the following to your legend call:
> ..., pch=16, col = c ("red", "blue"), ...
And remove the fill argument.
On 3/13/20, Ana Marija <sokovic.anamar...@gmail.com> wrote:
> I could make legend via this:
> qq(fdr2_sorted$FDR.q.val2, main = "RG_All", pch = 16,
> col=fdr1_sorted$group, cex = 0.8, las = 1)
> legend('topleft', legend = c('up-regulated', 'down-regulated'), fill =
> c('red', 'blue'),bty="o")
>
> but this gives me squares in legend. How do I write this code in order
> to have circles in the legend?
>
> On Thu, Mar 12, 2020 at 11:04 AM Ana Marija <sokovic.anamar...@gmail.com>
> wrote:
>>
>> Also how would I add legend to this plot?
>>
>> I searched qqman pages and there is no mention of that
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