Why some of the jittered points are in black in this box plot?

Question

I'm trying to make a box plot showing expression of Gene between types A and B. But I would like to color the points based on the List mentioned in the following dataframe "df":

Samples   Type  List    GeneA
Sample1     B   Other   -4.778968547
Sample2     B   Other   -4.63232938
Sample3     B   Other   -5.695251042
Sample4     A   Sample4  2.820003188
Sample5     A   Other   7.487856546
Sample6     A   Other   2.290055318
Sample7     A   Other   -1.183807203
Sample8     B   Other   -4.534681343
Sample9     A   Other   -5.140540608
Sample10    B   Other   -5.695251042
Sample11    B   Other   -5.695251042
Sample12    B   Other   -5.695251042
Sample13    A   Other   -5.071179371
Sample14    A   Other   1.117824251
Sample15    A   Other   4.42672296
Sample16    B   Other   -2.607036764
Sample17    B   Other   -4.154979727
Sample18    A   Other   -4.773270932
Sample19    B   Other   -5.695251042
Sample20    A   Other   0.472999278
Sample21    A   Other   -0.12535742
Sample22    A   Other   -4.32895912
Sample23    A   Other   0.342990853
Sample24    B   Sample24    -5.169967041
Sample25    B   Other   -4.628633712
Sample26    A   Other   0.18030665
Sample27    B   Other   -5.695251042
Sample28    A   Sample28    3.274762509
Sample29    B   Other   1.133797461
Sample30    B   Other   -0.489134592
Sample31    A   Other   -0.580311566
Sample32    A   Other   -0.801258402
Sample33    B   Other   -5.695251042
Sample34    B   Sample34    -5.695251042
Sample35    B   Other   -3.627831566
Sample36    B   Other   -5.126528687
Sample37    B   Other   -3.658755234
Sample38    B   Other   -3.563236707

I plotted the above data like following:

q <- ggplot(df, aes(Type, GeneA))
q + geom_boxplot() + geom_jitter(width = 0.2, aes(colour = List)) + 
  labs(y = "GeneA expression (logCPM)")

In the legend I could see the colors of the points. But strangely I see two black points for the Type B. Whats wrong here?

Answer 1

geom_boxplot plots outliers as black points. You can disable this with the outlier.shape argument.

+ geom_boxplot(outlier.shape = NA)