Add black outline for different geom_point shapes on DESeq2 PCA

Question

I am running a PCA with the DESeq2 package and would like to obtain a black outline on the shapes which are already based on an observation.The round ones work, but the other shapes do not.

Examples such as Make stat_ellipse {ggplot2} outline geom_point fill color or Place a border around points have data plotted as one only shape.

It is hard to give a reproducible example as it has previously performed a PCA on a big dataset, but this is what I have run the following:

ggplot(pcaData, aes(x = PC1, y = PC2, color = dFe, shape = location))+   
geom_point(size=5)+  
geom_point(aes(PC1, PC2, color = dFe, shape = location), shape= 21, colour="black", size= 5)

I believe the key is on the coding of that new layer of geom_point

Running scale_fill_manual I get the following

ggplot(pcaData, aes(x = PC1, y = PC2, color = dFe, shape = location))+   
geom_point(size=5)+  scale_shape_manual(values=c(21,22,23))

Just a quick thought, did you try plotting geom points with black color of some bigger size and again plotting geom points with color of smaller size? — Mohanasundaram, Nov 24 '20 at 15:54
I edited the image, so the size of the black outline is the same and coincides with the round shapes, but not with the triangles and squares, does this make sense? — Ecg, Nov 24 '20 at 15:58
`shape = 21` is overriding the shape aesthetic. Remove it. Use a `scale_shape_manual` to provide hollow (or bordered) shapes matching the locations. — Konrad Rudolph, Nov 24 '20 at 15:59
@KonradRudolph I edited the post, the outline changes but the fill is now gone... — Ecg, Nov 24 '20 at 16:12

score 2 · Accepted Answer · edited Nov 24 '20 at 16:36

2

As mentioned in my comment, use scale_shape_manual, and provide a fill aesthetic:

ggplot(pcaData, aes(x = PC1, y = PC2, fill = dFe, shape = location)) +
    geom_point(color = 'black', size = 5) +
    scale_shape_manual(values = c(21L, 22L, 23L))

edited Nov 24 '20 at 16:36

Ecg

908
1
10
28

answered Nov 24 '20 at 16:15

Konrad Rudolph

530,221
131
937
1,214

score 1 · Answer 2 · answered Nov 24 '20 at 16:10

1

Try This:

ggplot(pcaData, aes(x = PC1, y = PC2, shape = location))+   
  geom_point(size=7) + 
  geom_point(aes(x = PC1, y = PC2, color = dFe, shape = location), size=5)

answered Nov 24 '20 at 16:10

Mohanasundaram

2,889
1
8
18

Thanks, this is a good option! But the problem is when overlapping datapoint they don't show the full outline. But thanks a lot! – Ecg Nov 24 '20 at 16:17
1

You're welcome. @konrad-rudolph 's answer is the best. – Mohanasundaram Nov 24 '20 at 16:19

Add black outline for different geom_point shapes on DESeq2 PCA

2 Answers2