Ellipses for groups on PCA from DESeq2 - r

Question

I'd like to add in ellipses around my three groups (based on the variable "outcome") on the following plot. Note that vsd is a DESeq2 object with the factors outcome and batch:
pcaData <- plotPCA(vsd, intgroup=c("outcome", "batch"), returnData=TRUE)
percentVar <- round(100 * attr(pcaData, "percentVar"))
ggplot(pcaData, aes(PC1, PC2, color=outcome, shape=batch)) +
geom_point(size=3) +
xlab(paste0("PC1: ",percentVar[1],"% variance")) +
ylab(paste0("PC2: ",percentVar[2],"% variance")) +
geom_text(aes(label=rownames(coldata_WM_D56C)),hjust=.5, vjust=-.8, size=3) +
geom_density2d(alpha=.5) +
coord_fixed()
I tried adding an ellipse, thinking it would inherit aesthetics from the top but it tried to make an ellipse for each point.
stat_ellipse() +
Too few points to calculate an ellipse
geom_path: Each group consists of only one observation. Do you need to adjust the group aesthetic?
Computation failed in stat_density2d(): missing value where TRUE/FALSE needed
Suggestions? Thanks in advance.
> dput(pcaData)
structure(list(PC1 = c(-15.646673151638, -4.21111051849254, 13.1215703467274,
-6.5477433859415, -3.22129766721873, 4.59321517871152, 1.84089686598042,
37.8415172383233, 40.9996810499267, 37.6089348653721, -24.5520575763498,
-46.5840253031228, -4.01498554781508, -31.227922394463), PC2 = c(31.2712754127142,
5.89621557021357, -10.2425538634254, -3.44497747426626, 2.21504480008043,
0.315695833259479, -4.66467589267529, -4.27504355920903, -1.08666029542243,
-2.69753368235982, 5.89767436709778, -24.2836532766506, 4.43980653642228,
0.659385524221137), group = structure(c(4L, 5L, 6L, 7L, 8L, 5L,
8L, 1L, 2L, 3L, 6L, 9L, 9L, 9L), .Label = c("ctrl : 1", "ctrl : 2",
"ctrl : 3", "non : 1", "non : 2", "non : 3", "preg : 1", "preg : 2",
"preg : 3"), class = "factor"), outcome = structure(c(2L, 2L,
2L, 1L, 1L, 2L, 1L, 3L, 3L, 3L, 2L, 1L, 1L, 1L), .Label = c("preg",
"non", "ctrl"), class = "factor"), batch = structure(c(1L, 2L,
3L, 1L, 2L, 2L, 2L, 1L, 2L, 3L, 3L, 3L, 3L, 3L), .Label = c("1",
"2", "3"), class = "factor"), name = structure(1:14, .Label = c("D5-R-N-1",
"D5-R-N-2", "D5-R-N-3", "D5-R-P-1", "D5-R-P-2", "D5-Z-N-1", "D5-Z-P-1",
"D6-C-T-1", "D6-C-T-2", "D6-C-T-3", "D6-Z-N-1", "D6-Z-P-1", "D6-Z-P-2",
"D6-Z-P-3"), class = "factor")), .Names = c("PC1", "PC2", "group",
"outcome", "batch", "name"), row.names = c("D5-R-N-1", "D5-R-N-2",
"D5-R-N-3", "D5-R-P-1", "D5-R-P-2", "D5-Z-N-1", "D5-Z-P-1", "D6-C-T-1",
"D6-C-T-2", "D6-C-T-3", "D6-Z-N-1", "D6-Z-P-1", "D6-Z-P-2", "D6-Z-P-3"
), class = "data.frame", percentVar = c(0.47709343625754, 0.0990361123451665
))
As Maurits Evers suggests, I've added a group aes, which only drew ellipses for 2 of 3 outcome types.

Answer 1

Since you don't provide any sample data, here is an example using the faithful data.
The key is to add a group aesthetic.
require(ggplot2);
# Generate sample data
df <- faithful[1:10, ];
df$batch <- as.factor(rep(1:5, each = 2));
# This will throw a similar error/warning to yours
#ggplot(df, aes(waiting, eruptions, color = eruptions > 3, shape = batch)) + geom_point() + stat_ellipse();
# Add a group aesthetic and it works
ggplot(df, aes(waiting, eruptions, color = eruptions > 3, shape = batch, group = eruptions > 3)) + geom_point() + stat_ellipse();
So in your case, try adding aes(..., group = outcome).