I'm confused about the meaning of the black dots and the red shape in the violin plots from the seurat tutorial:
The black dots represent the values for individual cells. The "nGene" plot (the first one) shows the number of detected genes for every cell.
The red shape shows the distribution of the data. For the "nGene" plot, you can see that the average number of genes per cell is about 900 and most of the cells have roughly around 700-1100 genes.