Violin Plots

[Usha-88]

In this particular image,

what do the dots represent and what does the violin plot resemble? Since the Y-axis is termed as expression level, why cant we see a violin plot for 0,1,2 clusters even though there is some expression represented by the dots.

Thank you.

[samuel-marsh]

For more on violin plots you can find many resources easily via Google but here is paper cited by Seurat's function which describes it as well:
https://www.stat.cmu.edu/~rnugent/PCMI2016/papers/ViolinPlots.pdf
Another resource here: https://mode.com/blog/violin-plot-examples/

Each dot is a cell and the height of dot on y axis is the normalized expression level. The shape of the violin is based on the distribution/density of the data. In cluster 0 for instance there are only 4 cells which express the gene. The overwhelming majority of cells have 0 expression. Therefore the violin has no visible shape.

Best,
Sam

[Usha-88]

Does that mean, the multiple dots in clusters 0,1,2,3 have 0 expression of NKG7? Then why do the dots appear in these clusters?

[samuel-marsh]

Hi,
The dots that align with zero on the y-axis have zero expression yes. You can see this clearly in cluster 6 in which all cells have some level of expression of NKG7 and therefore there are no dots at zero.

Best,
Sam

[Usha-88]

Thank you.