Violin Plot
I'm doing a gene expression analysis study and I used violin plots for the hub genes expression profiles. I need some explanation to understand this plot, especially regarding the density (width and peaks of the violin). I couldn't understand what the density represents for each hub gene in each plot.
Thank you in advance
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leenkhoury282 •
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Hard to tell with so little details. What type of data is this? are you using a built-in function from a package to make the violin plots?
i'm using normalized mRNA microarray expression profiling data and the violin plots were generated by ExpressAnalyst (https://www.expressanalyst.ca/ExpressAnalyst/home.xhtml)
Generally speaking, the violin plot is a density plot, which is sort of like a smoothened histogram.
The width of the violin plot is a representation of the amount of points found at a certain value.
I am not familiar with the data you reference but in general, violin plots are used to show gene expression values on the Y-axis and conditions on the x-axis. Usually each plotted point is the expression value for a separate gene, and then the violin summarizes this information in a density plot. Using this assumption and just judging from the density curves of the violin plot, in CONTROL condition it appears most genes have ~9.4 expression value, with no genes >10 and no genes < ~9.2 expression values.
However, if the individual points shown on the plots represents all genes that were plotted, I don't think a violin plot is really needed here, and may even be misleading.