How to smooth (ggplot2) 3 samples in the same plot

Question

[Lila M]

Hi everybody,

I want to smooth 3 different samples and see the result in the same plot. For that propose I'm using ggplot. I can plot the 3 curves in the same plot , but when I've tried to smoothing them, I have to make it separately, as follow:

c <- ggplot(d3, aes(x = bins, y = sample1, color="sample1")) + labs(y = "Coverage", x = "distance to TSS")
d <- ggplot(d3, aes(x = bins, y =sample2, color="sample2"))+ labs(y = "Coverage", x = "distance to TSS")
e <- ggplot(d3, aes(x = bins, y = sample3,  color="sample3"))+ labs(y = "Coverage", x = "distance to TSS")

    c + stat_smooth(span = 0.2) 
    d + stat_smooth(span = 0.2)
    e + stat_smooth(span = 0.2)

Is there any way to plot the 3 smooth samples in the same plot?

Thank you very much

Answer 1

[Devon Ryan]

Have you tried further collapsing the d3 data frame such that sample is a column with levels sample1, sample2, and sample3? That would solve this (you'd color or fill by sample then). You can use the tidyr package to tidy your data frame.

[Lila M]

Now I have a data frame like this:

Bins   Sample1    Sample2  Sample3
1         0.54            0.59            0.41
2         0.62            0.75            0.13 
3         0.76            0.97            0.50
4         0.21            0.43            0.53

Are you suggesting me to perform a data frame like:

Bins     Samples      Coverage
1           Sample3        0.13
2           Sample1        0.21  
3           Sample3        0.41
4           Sample2        0.42

.....

Thanks!

[Devon Ryan]

Yes, then you can use either stat_smooth() or geom_smooth() (they're essentially the same thing) with aes(color=Samples, fill=Samples). ggplot works best with "tidy data" (google "R tidy data" if you're not familiar with that concept).

[Lila M]

Thank you Davon, I know hot to plot them after tidy my data, the problem is, that I don't know how to tidy it. Is the first time that I come across with this problem. Any suggestion for my starting?

Thanks!

[ddiez]

Take a look at the tidyr package. In the vignette you have a nice introduction.

[Lila M]

Thank you, I've used gather and arrange functions and now it works perfectly!!!!! thank you very much for your advice!

[Joe]

If you're just trying to add a smoothed series to the plot, have a look at the geom_smooth() aesthetic.

[Lila M]

I have a look, but I didn't find anything useful...