Entering edit mode
9 months ago
leenkhoury282
•
0
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
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.